Does someone know why chain drifting is sometimes not done even if you could easily get two mts. This happens on CM on the stairway turn after the shroom cut, on KC in the water current in the tunnel and on rMC right after the straight-away with the piranha plants.

Because it forces you to take a wider line. Also in KC miniturbos are less effective when you're in the current

I'm assuming this is because mts have a speed cap independent of other speed boosts. If that's the case, what boosts does it apply to? I know mts aren't effective when in a shroom, boost panel or trick boost, but what about things like slip streams or stars?

It doesnt matter what your speed is, an MT will always take you up to the same speed. In a current in KC you already have an increased speed so they are less effective