As long as (1) you are in compliance with the Residency Obligation on the date you make the PR card application (which you appear to be as of today), (2) are settled and living in Canada, and (3) will be mostly staying in Canada while the PR card application is pending, there is no reason to delay making the application for the new card. OTHER FACTORS will have more influence in whether the application encounters non-routine processing and related delays.
Margin over the minimum RO is less significant than, say, having a margin over the minimum presence requirement in qualifying for a grant of citizenship. After all, even if you wait until you have been in Canada 825 days within the relevant five years, that means you have been OUTSIDE Canada more than IN Canada. So waiting longer to apply for a new PR card is not likely to offer much insurance against non-routine processing.
Waiting until you have spent 730 days IN Canada, rather than applying today, may make your case a little stronger, but the emphasis is on that only making it a little stronger. (See below discussion specifically about RO compliance.)
Re-entering Canada Without Valid PR card:
A PR has a statutory entitlement (some call it a "right" but it is not the same as a Charter "right") to enter Canada. The CBSA border official was correct . . . except actually you do not even need a copy of your CoPR. And, by the way, your expired PR card is probably better for this purpose than a copy of the CoPR.
As long as somehow (and private vehicle is the usual way) you reach a PoE into Canada, you will be allowed to enter Canada. Proof of identity (passport) should suffice. Better to have the expired PR card, or a copy of the CoPR (keep original in safe, secure place), but as long as you establish who you are, you will be allowed in.
A PR needs a valid PR card (or obtain a PR Travel Document) in order to board an international flight headed to Canada (and even this does not apply to PR's carrying a U.S. passport).
Impact of Self-employment History:
This may or may not trigger questions. It is far more likely that how things go, and in particular whether you encounter non-routine processing, will depend on a wide range of factors and how they can influence each other. But sure, some concerns, some questions may be triggered by your travel history in conjunction with the employment history, for example, particularly in combination with
cutting-it-close in complying with the RO (that is, spending more time abroad than IN Canada). This is one of those
it-is-what-it-is elements.
Non-routine Processing:
"I suspect that if i apply right after my residency obligation is met, it might go for secondary review and i might be asked to submit additional documents and will delay the process, might as well apply in May . . ."
Note that there are various types of non-routine processing for PR card applications. While factors related to RO compliance can trigger Secondary Review, which tends to delay the process for quite a long while, that often (perhaps usually) does NOT result in requests for additional documents and is typically NOT focused on evaluating RO compliance. Many forum participants refer to other types of non-routine processing, including in particular RQ-related processing (which does involve requests for additional documents, typically to establish the PR was in Canada enough to meet the RO), as "Secondary Review." Label does NOT matter.
But sure, since you will be cutting-it-close, whether you apply for a new card in January or May, there is a RISK your application could be referred for Secondary Review (which can mean a delay in getting a new card for many months, even a year), or referred to a Local Office for a RO compliance investigation, or otherwise a risk you could be asked to submit additional documents to show your presence in Canada and compliance with the RO. Waiting to May may reduce the risks, the odds so to say, but probably not by much . . . and probably not result in getting the PR card sooner (note, in contrast, I often emphasize that waiting to apply for citizenship longer can result in taking the oath sooner).
Compliance With the PR Residency Obligation:
FIRST, some clarification about meeting the RO. To be clear, there is NO SUCH THING as "
completing" compliance with the RO. I get what you (and many others similarly) mean, about reaching the threshold of having spent 730 days IN Canada (usually in reference to 730 days in Canada since landing). And sure, that has some significance. Reaching that threshold insures there is no breach of the RO, and that there will not be a breach of the RO until, at least, the fifth year anniversary (after that, days IN Canada more than five years past no longer count).
BUT remember, each day involves a different calculation of RO compliance. Most everyone readily gets this in reference to RO compliance calculations for dates after the fifth year anniversary. But it also applies from the first day after becoming a PR (on that day the PR has a credit toward RO compliance of 1825 days, and for the next five years it only gets lowered by the passing of days OUTSIDE Canada).
Thus, for example, if you anticipate leaving Canada between now and the fifth year anniversary of the day you landed, in May 2021, your RO compliance calculation is higher today than it will be in May. Right now your RO compliance assessment gives you credit for every day you have been IN Canada, so far since landing, PLUS all the days left on the calendar between today and that 5th anniversary day in May. It will be similar in January, if you anticipate going abroad between January and that 5th anniversary day in May.
In contrast, for example, if you do not leave Canada at all between today and May, your credit toward complying with the RO is precisely the SAME as it will be in May. Even though you have not even spent a total of 730 days IN Canada yet.
This is NOT to suggest applying for a new PR card BEFORE reaching that threshold of 730 days IN Canada since landing. Yes, it is probably better to wait until then. As long as you wait that long, there is no need for IRCC to check to see if you have additional absences after you made your application.
A wrinkle or so in your account of the facts.
At the risk of making a bigger deal than it deserves . . .
"I came back to Canada mid 2018 and have been in Canada majority of the time and traveled to US to meet friends and family once a month or two. I will complete my 730 days Residency Obligation by Jan 2021 . . .
. . . in May . . . i will be over 825 days in Canada . . . "
It may come across as quibbling, but if in January 2021 you will have only spent 730 days in Canada since mid-2018, you have been outside Canada at least six or seven months since mid-2018. That's more than occasionally meeting family and friends abroad. I am not challenging your account or characterization of things. I am, nonetheless, suggesting being more objective and less self-assuring in how you look at and characterize things, especially if you want frank and honest views about things like the prospect of Secondary Review or other non-routine processing.
Again, this is not worth making a big deal about.
Your facts look FINE. But it is a very common mistake, looking at things from a self-assuring or even self-serving perspective, failing to be objective. To be best prepared for what could be coming (not necessarily what will be coming, but what might be if there are problems), far better to be coldly, if not brutally objective. For you, for example, given the nature of your employment (in many respects, at least similarly, I've been there, done that . . . a big reason I waited a full extra year to apply for citizenship), you will want to be sure you have extra good records, just in case there are questions. Not suggesting there will be. Again, your facts look fine. Just in case.