I think the guidance of the manual on which way to load the film should be determinative. They are likely aiming at giving you a scan that shows the image as it is intended to be seen. So start with that.
I agree with Mark that there may be a reason why Canon specifies it as they do, but it may also be something as trivial as an over-simplification in their software that doesn't allow to see the image right side up, mirrored. I don't know their software well enough. Anyway, VueScan has all those possibilities, so I'd go for the common practice of positioning the film with emulsion side towards the sensor, unless there is a mechanical reason like in the film holder e.g. to avoid Newton's rings.
As for the business about native resolution, I would subject the grain-aliasing risk to an empirical test. See whether anything like that shows in your prints by "right-sizing" the scans, before hogging huge amounts of storage with vastly over-sized files relative to your requirements. Bart can explain or point you to references about the risk of grain-aliasing given his expertise in the matter, but what matters most in the final analysis is what you see.
This is
the original article that warned about grain-aliasing when scanning at lower that native scanner resolution.
Here are some comparisons between grain-aliasing from scanning at a lower PPI and downsampling to that same PPI.
Norman Koren has also written about
grain-aliasing, and also mentions the influence of the resolution limitations of the scanner optics to even resolve such level of detail (the lens limitations can function as a high-pass filter), and noise reduction software to mitigate the artifacts.
In my experience, there is also film resolution to be had above 4000 or 4800 PPI. My 5400 PPI Minolta scanner extracts quantifiably more resolution from the same image of a test target compared to lower (4000 PPI) resolution scans. I got the following resolutions from three different scans of the same test target shot on film: Nikon LS2000: 45.4 lp/mm, Nikon LS4000: 62.1 lp/mm, Minolta SE5400: 76.1 lp/mm. That additional resolution also helps if one wants to use noise reduction software, because that usually loses a bit of resolution. Of course not all images that were shot handheld will have such resolution, and not all (camera as well as scanner) lenses perform as well, but reducing grain-aliasing also allows to use more sharpening.
Cheers,
Bart