The dyes used in textile dying are each according to the fiber being dyed. So, you will have one formulation for polyester, another for cotton, another silk, another for rayon, and so on. It has nothing to do with whether a yarn is a microfiber or not.
If two towels are from the same maker, one dark one light, and one feels different than the other, then they used too mych dye on one. There should be no difference in the feel if the goods are dyed and fixed properly.
Generally speaking, the reason to keep away from dyes is because many cheaper dyers don't "fix" the dyes properly so they can transfer to the finish. If they are properly fixed and not dyed to excess, then you should be OK. As a rule though, keep away from colors that have a tendency to run such as red and red families, navy, and fluorescents.