I am not "proud" of being a gear snob (neither is my wallet), however, I do enjoy nerding out on tech and off shoot builders and stuff the general public is not familiar with. Jeff has a great sound, so the Boss stuff is working for him. What I am trying to say is if I were in his shoes and was part of an amazing project like Isis that has some money and the ability to be endorsed, I would have gone more boutique and off the wall than a Boss pedal.
IF his Boss pedals are all circa made in Japan era and unique pieces like the PS-3, then I can get behind it. Looking at the Amplification Isis uses (Aguilar, Fryette/VHT, beat to s**t cabs/boutique cabs...) and the crazy Electric Guitar guitars they are playing on, one would just assume they would have more unique effects gear than something you can get from just about any music shop.
As to Nerotic's reply of "why change it?", I'm not saying to change it. The first time I saw his board after a show, I was shocked that he WAS getting those tones from Boss. TB has opened up my eyes to all the amazing pedal builders of the world and thats why I "always wondered why he uses Boss", with all the other flavors out there.