Hi, I can't answer precisely, but I can point you at some things. At first glance, it would appear that your scenario 2, simple contrast differences in the colored dye layers, would be the predominant problem (when changes are made to film process temperature, time, etc., the top film layer tends to be affected the most, etc.). But... films like Portra do other little color-correcting things along the way - they have things called DIR color couplers, that when released will inhibit further development, perhaps in an adjacent dye layer. Or between certain layers, certain chemical scavengers might "mop up" chemicals trying to cross between color layers, etc. So this sort of thing, when disrupted, falls in your scenario 1, "channel mixing." I wouldn't expect either of these things to be TOO severe, as long as you are close to the aim temperatures. But I don't really know.
The next thing is the scanning stage, which is off-topic for Apug (sorry). But your scanner likely doesn't see the film exactly the same way as the paper does, so needs certain corrections. Although the film's orange mask and the DIRs, etc., mostly correct the film for optical printing, your scanner probably needs to use a corrective "matrix" in the software, it ought to come from one of the manufacturers who knows how to figure it.
If I were in your shoes, the first thing I'd do is to evaluate my film processing. In commercial processing they'd run special test strips, aka "process control strips" supplied by the manufacturer, then read with a densitometer. In your case, what you might do is shoot a double set of test images, then have one roll processed by a trusted lab (you presume that they are in spec); you do the other roll yourself, hoping that it's close to a dead match.
If you want to get a rough idea of what various process errors do to C-41 film, look for Kodak's Z-131 manual. The last part, on process monitoring, shows how the control strips behave under certain conditions. If you're familiar with the "characteristic curve" of film (aka H&D, or D log E, D log H, etc.), the control strips "LD" point is fairly low on the curve, and the HD point is fairly high. So when they plot "HD-LD," this is a measure of contrast.
Best of luck. This is certainly no turn-key operation.