Not much risk. This is not something a processing agent will notice until the interview and review of your passport. As you note, it does not affect the calculation of days present.
Since the passport stamp will be a date your calculation shows you to be outside Canada, any question about it is readily resolved. Probably something to take note of and be prepared to proactively explain (as you do above and before asked any question about it) at the interview.
Caveat: for clearly qualified applicants, the interview can go much faster with minimal opportunity to interject than many might anticipate, which would be OK, in which case you explain if asked and otherwise it is not something to worry about. Oft times the interviewer can ask a question about the presence calculation, such as "is this complete?" or "did you take any other trips?" or something along those lines. If asked something like this, that would be a perfect opportunity to clarify that you declared the trip to the UK xx date and during that trip you also went to South Africa for a safari (nice work if you can get it, revealing some green in my gills).
Note: the duration of the trip while on a trip otherwise declared is not something that is readily apparent . . . the passport stamps, however, are what are readily apparent if and when an interviewer is closely examining them (whose passport gets the more thorough screening varies, not all do). Those should have readily identifiable dates. Those dates should easily be compared with dates in the presence calculator.
One more caveat: obviously, if your trip to South Africa is prominently noted in social media or other Internet venues, that is a situation in which it is possible, probably NOT LIKELY but possible, an IRCC processing agent might have come across it and noticed it was not disclosed in the presence calculation. Who and when applicants are subject to such online, open source inquiries, we do not know. We just know that some are sometimes. Just something to be aware of.