I think that it's just that the company is conservative...they don't want a failure, and they are sure it works with an unmodified. If a modified is used, and it hasn't dried properly, you can compromise the bond - I don't care whose membrane you use - moisture doesn't go through it, and neither does it go through the tile (at least very fast), and it WILL take excessive time to properly bond. If the tile is disturbed before that happens, you can have a bonding failure. A modified between impervious surfaces is almost like a mastic...on larger tile, it can take weeks to dry out and approach what an unmodified achieves in a day. How many people are going to stay off the surface for that long? Yes, the rapid set stuff (at least the cement part) cures rapidly, but if properly mixed, those sand and cement particles are coated with the modifiers, which don't reach full strength until they dry.
While many people may know you should remix a modified after slaking, most (IMHO) do not know why. The modifiers must hydrate so they can flow properly to coat the sand and cement particles. That happens, not in the first mixing, but after slaking and during the re-mix - they absorb the moisture and become stickier and can flow while remixing. If the second mixing is done too soon or ommitted, the thinset will be considerably less strong and have a very different texture from when the instructions are adhered to. Some people tend to add more water than specified trying to get the texture what they want. This weakens the mix. If the proper mixing, slaking, and re-mixing times are adhered to with a proper paddle and speeds, they'd most often find the prescribed water content is right on. This info comes from manufacturer's reps as received at a class at the TCNA school. Old habits die hard, and many people (pros included) do NOT mix their mortars per the instructions. They'd be surprised at the differences if they did.
It is a tribute to the mortar manufacturers that ANY modified thinset works when sandwiched between a waterproof membrane and a highly impervious tile.