I don't wrestle much with how it should be, other than extrapolating from the law and rules in conjunction with what we know about actual practices (based on multiple sources, from IRCC online information to official accounts of actual cases in published Federal Court decisions, along with scores of anecdotal reports), to figure out, as best we can, how this works. Threads like this one, in particular, are generally focused on sharing information about how things actually work, to help applicants better navigate the process (in contrast to the scores of other threads here oriented to venting or criticizing, which has its place but which can be a distraction, in a topic like this, for those just trying to figure out what to expect and how to best approach things).
My sense is it helps to focus on and keep how-it-works separate from how-someone-thinks-it-should-work, particularly for those who are making personal decisions, and sometimes trying to navigate making tough choices, and who otherwise want to prepare for what might happen. If interviewed, all applicants should be prepared to answer questions about where they live, they work, and where their family members live. And those applicants known or perceived to be abroad (which of course is made apparent if the applicant takes the test while abroad) can anticipate they, in particular, are more likely to be asked such questions in an interview.
And for me, just keeping up with how-it-works, as best we can sort out (a lot about the nature and scope of IRCC's questions and internal decision-making is kept behind the curtain, not at all accessible to the public), can be challenging enough.
As for individual entry-exit records maintained by CBSA, IRCC primarily uses that information ONLY to check the accuracy of what applicants submit, or in contested cases to challenge the applicant's account. What that means is that if the CBSA information more or less affirms what the applicant has declared, that will be a big factor in helping IRCC make an inference the applicant was present in Canada not just the days they went through border controls, but in the days between a known date of entry and the next reported date of exit.
Many, if not most, assume that days following a date of entry count, counting all the days after the entry up to and including the next date of exit. And that is how the online presence calculator works, in effect making an inference of presence all the days in-between entry and next exit. Moreover, the vast majority of applicants generally benefit from this inference, BUT it is important to recognize that is only so long as IRCC has not found a reason to question the applicant's travel history. (IRCC's decision-making mostly depends on what the applicant reports is their travel history, going favourably if CBSA and other information indicates the applicant's account is reliable, going the other way if CBSA or other information indicates any reason to question whether the applicant's account is complete and accurate.)
There is, of course, some solid reasoning underlying the inference of presence between entry and next exit dates. Not many (at least not in terms of a percentage of travelers) exit or enter Canada without CBSA capturing a record connected to the PR's client ID. Nonetheless, Canada's border is notoriously porous and IRCC makes no inference that CBSA records are complete.
So, for now, despite employing this inference in the calculation of days, as calculated by the online presence calculator, it is NOT an inference IRCC employs unless there is sufficient corroborating evidence documenting actual presence supporting that inference (to a standard we do not know), evidence showing actual presence in-between travel dates. Hence, the requirement there be no gaps, none at all, in work or address history. And it does not take a whole lot to trigger RQ-related inquiries (just a few errors in the travel history can do it, or some concern about the applicant's actual employment history, or a combination of factors in which, yes, living or working abroad after applying can have significant influence).
IRCC could rely more on the CBSA travel history information. Many believe IRCC should. For now, HOWEVER, that does NOT appear likely to happen, at least not anytime soon.
Applicants would be wise to be aware of this, and to wait to apply with a buffer appropriate for their particular situation (not only was I self-employed, but I was providing services to businesses outside Canada, so I waited a full extra year to apply), to be as sure as possible the travel history in their application is complete and accurate, and to be prepared to document where they were and what they were doing in Canada in-between dates of entry and the next reported date of exit. And to be prepared to respond to a wide, wide range of potential questions about them and their lives, right up to when they are in an interview.
And these days, as it appears that Trudeau's turn at the helm is likely on a course headed toward retirement, voluntarily or otherwise, there is a rather substantial prospect that a Conservative government could be coming sometime soon, and Pierre Poilievre could be our next Prime Minister. Despite some moderation in rhetoric during his campaign for the leadership role, Poilievre is very much a solid former Reform Party, Alberta/Calgary rooted conservative, whose ties to Harper and Jason Kenney (one of the key architects of measures targeting those perceived to be applying-on-the-way-to-the-airport, the Minister who adopted drastic triage criteria making things like a recently issued drivers' license a stand alone trigger for full blown RQ) go deep, and who from most accounts is probably even farther to the right and more anti-immigrant than Harper or Kenney. If that happens, no advanced studies in political science necessary to map the trajectory of IRCC's handling applications by those known to have moved abroad.
While to a large extent the jury is still out about the nature and scope of current practices in regards to applicants known or perceived to be abroad, those affected would be wise to be prepared for more probing interview questions, and prepared for significantly more inconvenient hurdles on their path to taking the oath -- this is not to say how many will run into this, again the jury is still out and we just don't know -- but it is to say those affected should consider being prepared.