Great question! And if keep asking every 3 months or so I’ll probably just keep giving different answers. But this is what I have done for myself, bottom line r1-r3 on or off it sounds great.
1 If playing with my full rig I can control it any way I want using my Rockman midi octopus and my Rocktron All Access foot controller the real power is in the All Access.
I usually don’t use the EQ it with r1, when playing something funky tends to break up a bit between me hitting hard and my humbuckers but there again depends what I’m doing
With r2 I favor the EQ being on, just shapes that channel especially, so nicely, there again depends on what I’m doing
With r3 I kind of use it as an additional rhythm channel and when the EQ is kicked in a lead channel. This is the channel where I’m happy either way. You know in the case of my rig I should even use the words (lead & rhythm channels) its just a different sound really, my processor can give additional boost for a solo and some EQ if desired.
2 If playing with just the FU-3. (Which I play bone dry allot) It can be complicated grabbing all 6 configurations on the fly so I compromise. The EQ is on Auto for r2, for r1 the EQ is off and of coarse r3 there is no compromise, either way on the switch. Of coarse if a song calls for it the EQ for r1 is no problem.
Like I said ask in 3 months as far as a full rig that answer will be the same but using just the FU-3 that answer will probably change