How do you mess up answering an extremely simple yes/no question? Respond to IRCC ASAP with the information they want. No point thinking about consequences. What's done is done.
Missclicks happen... But people are too eager to submit without reading everything again.
For OP, in the order of your questions :
1) probably, but doesn't really matter. Everyone's application is separate.
2) it already affected it obviously, but refusal would be a stretch. If you provide a convincing answer, they should validate your physical presence at some point. "At some point" could either be relatively quickly after your answer, or they may take a very long time. You don't control how it goes.
3) No need for the CBSA report I think, IRCC has access to it, they based their request to you on it after all. What you need to do is to provide an updated physical presence calculator. Use this :
https://eservices.cic.gc.ca/rescalc/resCalcStartNew.do?lang=en
4) Well, we can never completely rule out something, but mistakes happen. In the explanation letter, apologize, acknowledge your honest mistake, say that you went too fast while filing it and be very clear that your physical presence wouldn't have been a problem on the day you signed your application had you now screwed up that section. Also, you may want to stress that the rest of the information you provided is absolutely correct, and that the physical presence is the only factual mistake (obviously, only if you can say so...!) By being apologetic, truthful and precise is your answer, chances are IRCC will just chalk it as "careless applicant". There are plenty of those after all. It would be a different story for someone who forged a diploma, put wrong information willingly (kinda hard to plead carelessness if someone actively writes that they live in Toronto when their LinkedIn specifies that they have a non-remote job in Singapore for example), but I wouldn't sweat it too much if I'm you.
Also, as far as being honest goes, since you say here that someone else filled your application, IRCC probably doesn't need to know I guess. Own the mistake alone. Plenty of people help family with their application without the need to add the representative section (including me, did so for 2 family members of mine, although in their presence and I validated every single answer and all), and that's fine, but you're responsible for what you sign. Oh well. Good luck, chances are this will mostly end up being a bump in the road, and you may become a citizen later than when you would have, had you taken 2 minutes to proof-read the application, but you should be fine.
Long story short :
Good explanation letter : absolutely
Passport copy : yeah sure
Flight tickets, hotels or airbnb proofs : yeah why not
CBSA report : probably overkill, but a new physical presence calculation that matches both reality and the content of that report is a must!
Good luck.
