I can understand how contrary much "indie" is to the tastes of a diehard fan of prog. Also, I assume the meaning of indie here is more referring to the music that has its roots in punk/new wave. But the idea that that sort of indie is somehow not experimental or whatever is ridiculous. It just experiments in a different way. Prog with complexity, indie with simplicity and minimalism.
Tool, though, from the standpoint of rock/prog history, ought to be considered (at least as far as their 2/3 better albums go) as a good, even virtuosic, band within the genre. That goes without saying, in spite of my personal dislikes for the band.