With color negs there is a very real danger of retained silver which can make fine tuning the final image quite a bit more challenging. I was fortunate in that I had hand processed all of my 35mm color negs. And had properly controlled developer strength and slightly over replenished the bleach bath. Regardless expect to spend some time developing a good touch in finding the correct color balance from negs.
I won't say it CAN'T happen, but it would have to be a really sloppy commercial lab to have any silver remaining in a color image. Maybe the old mall parking lot labs stretching things to the limit could have it off enough for it to happen, but I don't see any halfway reputable lab letting their bleach get that bad. It's also helped by the fact that bleach is the least finicky of the steps and most bleaches thrive on oxygen exposure.
Where it can be an issue are with Blix-based at home processes(or the old Tetenal press kits). Blix basically balances on a knife edge for both operations to work properly, and it's not helped that many people using them stretch them to their limit.
Unfortunately, almost all home kits these days use Blix(Kodak-branded 3-bath C-41 is finally back on the market...). Tetenal marketed them to photojournalists to use in hotel bathrooms-more fast and convenient than long lasting.
I went APSc because the macro lens focuses to 1:1 on a full frame. On APSc I can crop a bit in camera and there is still enough headroom for the auto focus to perform flawlessly. With full frame probably best not to work right at 1:1, rather leave a bit on the edges so the auto focus can do its thing, then do a bit of cropping post image.
I'm not really sure I'm following this.
Yes, with APS-C you're using the lens at less than 1:1. Still, though, I've never had an issue with autofocus working all the way up to 1:1 with any of my DSLRs even with my ancient Micro-Nikkor 105mm f/2.8D or Micro-Nikkor 200mm f/4D(latter not recommended for copy work...).
With that said, if working at 1:1 with any subject, usually the best practice is to manually focus the lens there and then adjust camera/subject position. For film/slide copying, Nikon at least makes an adapter to fit the end of one of the micro lenses(I think the 60mm?) and hold film/slides at the correct position.
If you're saying that you can crop in scanning...well at least a decent chunk of the full frame cameras out there now are 40mp+, which for an older generation faster color negative film, that should resolve the dye clouds...