I've off-roaded my GX quite a bit and scuffed up and drug my ARB skids, but have yet to whack the Y-pipe. The Y-pipe (and whole exhaust itself) is pretty flexible due to being mounted on the rubber isolators and having a rounded donut gasket where it meets the catback, so even if you do whack something, it should just temporarily deform the whole system and then drop back down. I would personally not want it in that Tacoma location due to cooking the CDL actuator, and it's more in the middle of the rig where it's more likely to get whacked (apex of the breakover angle) when going over a big rock.
You could also just add to and subtract length from the the hangers for the Y-pipe and catback behind it to get the Y pipe up above the ARB skid, which should be a pretty easy welding job.