Remember that the Gain and all the EQ settings are somewhat interactive, so swapping these pots should have an effect on how they work together. It's all connected.
I wouldn't say the mod makes Ch2 cleaner at all... I'd say if anything it makes it
clearer. By that I mean, EQ-wise, less prominence in the low-mids; somehow the taper of these pots moves the emphasis between these two basic curves (Ch1's slight scoop, and stock Ch2's big mid-hump).
In terms of the amount of gain or drive on-hand... there's still tons, and post-mod I feel like I can use WAY more gain than I was comfortable with before; simultaneously, the lower-gain settings are also more usable than they were. The added brightness makes the channel stylistically meaner, grittier, with a sharper edge, but it can be dialed out too. Stock, I would have described it as more buttery smooth, and yes, darker; it was harder for me to get the brighter edge under that configuration.
As has been mentioned, theoretically it's possible to get all the same sounds under either setup; I think it's then a question of usability and taste, in other words, which angle to you want to approach the channel from -- one that's characteristically darker, but can be tweaked to get the brighter effect; or one that's characteristically brighter, with the capability to dial out the brightness if so desired? I like the latter myself. But that's just me.