Some further observations:
CBSA preference is that travelers present the document/identification which best shows the traveler's identity and status in Canada; for a PR this is simply a valid PR card. (Prior to becoming a Canadian citizen, I presented only my PR card when entering Canada by car, and was never asked for anything more; only secondary referrals were for customs on those occasions where I needed to pay duty/HST for goods I was importing into Canada.)
For a Canadian PR, when driving into Canada, there is no advantage gained by presenting the U.S. passport at the PIL line. Border officers will sometimes ask to see additional documentation, such as the traveler's passport, but for the vast majority of routine travel the PR card suffices (again, it is the preferred form of identification for PRs) and usually facilitates the fastest PIL processing, resulting in what is essentially being waived-through.
Obviously, various circumstances can trigger additional questioning or document requests, and may trigger a referral to Secondary for an immigration interview. How things go at the PoE is very individual specific, very much dependent on the individual's particular circumstances, immigration history (including border crossing history, which may include which PoE has been used), and can range from some additional, simple and easily answered questions at the PIL (usually a drive-through booth), to a referral for a Secondary examination.
Example I: If the PR presents a form of identification other than a valid PR card, that can invite further questions. The nature and extent of further questions can vary greatly depending on the form of identification presented, the individual's particular circumstances and immigration history, and other factors. Canadian PoE officers are generally friendly and lenient when dealing with U.S. citizens, so a PR presenting a U.S. passport does not, ordinarily, not-in-itself anyway, trigger concerns . . . unless there are other factors which invite some questions. If the PR's border crossing history, for example, indicates there could be an issue about PR Residency Obligation compliance, that is something tending to elevate the scrutiny and potentially lead to a Secondary examination regarding the amount of time spent in Canada.
In some instances, presenting a passport (without presenting a PR card) may trigger a referral to Secondary to verify identification and PR status, but for PRs who are U.S. citizens the computer screen at the PIL will, usually, readily verify the PR's status in Canada. The PIL officer is likely to ask one or two additional questions about status in Canada, such as asking the traveler what his or her Canadian status is, or specifically asking if the traveler is a PR, and if so, why the PR card was not presented. But honest and reasonable responses to such questions should suffice and not (in the absence of other factors inviting further questions) lead to more extensive questioning or a referral to Secondary.
Example II: The vehicle being driven can be a big factor. When the PR is the owner-driver of the vehicle, where that vehicle is registered can influence how things go. A U.S. registered vehicle, for example, informs the PIL inspector/officer that the owner resides in the U.S., not Canada. Since the purpose of granting Canadian PR status is to facilitate permanent residence in Canada, that can invite questions. But even as to this, the nature and extent of any further examination will depend on many additional factors, such as other factors which could indicate compliance, or non-compliance, with the PR Residency Obligation. Another factor is the history of crossings, both relative to the individual and as to that vehicle. While being examined more closely resulting in satisfactory resolution of any questions does not guarantee there will not be a similar examination the next time, more often than not once in-effect-cleared, the next time it goes easier (CBSA generally, albeit not always, tends to avoid re-examining or reconsidering or revisiting things).
In contrast, driving a self-owned vehicle registered in Canada is a factor which can make the crossing easier and go more quickly, especially the second or third time the PR crosses at that same location using the same Canadian registered vehicle.
Credit toward citizenship for days in Canada:
The person applying for citizenship is required to declare all travel in and out of Canada. The burden of proving these dates is on the applicant. PRs should keep precise records of all trips across the border and to other countries.
Generally IRCC (formerly CIC) will, as you say, credit all the days an applicant reports being in Canada. IRCC primarily relies on the physical presence calculation submitted by the applicant.
IRCC will, of course, examine that information and compare it to other information, including as to consistency with the rest of the information provided by the applicant and with the applicant's immigration history, but also consider other sources of information such as the individual's travel history maintained and provided by CBSA. IRCC is looking for discrepancies, for indications the applicant's declaration is either incomplete or inaccurate.
If IRCC identifies any reason to question the applicant's accounting of travel, then IRCC will not necessarily credit all the days an applicant reported, in the physical presence calculation, being in Canada. Rather, IRCC may then require the applicant to provide more information and supporting documentation (evidence) to prove the number of days the applicant was in Canada. This can be difficult for some applicants. And of course extended time working abroad, including in the U.S., tends to raise doubts, not just questions, about the extent to which the applicant has completely and accurately reported all time in and out of Canada.
Keep exact records of ALL travel dates. Keep some documentation to prove dates in Canada. Make sure to have a comfortable margin above the minimum requirements (these are likely to change in the near future; current requirement is a 4/6 rule; proposed change is for a 3/5 rule).
It is also prudent for PRs with extensive absences from Canada to also keep such exact records even if they are not anticipating making an application for citizenship. Any PR may be challenged to prove compliance with the PR RO.
