sorry for the slow response....my internet was down all day.

the crazy thing about these presets, is pretty much what you are saying; adjusting one thing like gain also tweaks tone.

so you pretty much have to try one of three thing to adjust gain:
1) preamp gain of course. but on some amps it changes the tone because i'm using the master volume to push the poweramp stage.

2) the master volume on many heads acts like a variable mid control, plus it adds gain. i set most heads up to push the power tubes into overdrive, then dial in the gain with the gain control. once the gain is set about like a "standard" head, i tweak the eq accordingly. the reason i do it this way is because the power amp section changes tone as it distorts; it's more scooped mids when the guitar volume is rolled back, but more full in the mids when cranked. this is one of the single most important things about these new head mods.

3) the pre-eq output control will normally do close to the same thing as the gain control....but try it anyway and see if it works for you. i am using the pre-eq to cut bass and in some cases highs too, and boost mids. if you lower an amp's gain, you will probably need to go into the eq and change the amount of low end i'm cutting.

and yes, i realize that there are no power tubes nor preamp tubes in the eleven rack...but these new presets have me wanting to pop the cover of the eleven rack to make sure there are no tubes burning.