Hrmm. My dear I hate to do it, but I must disagree with you; gain does affect tone, and the relative gain of the pickups does have an important effect. I find that I like to keep the pan centered but bring up the gain on the neck pickup just a bit (which is not the same effect as bringing down the gain on the bridge pickup).
[I wish the gain controls were still front mounted and if I ever order a custom, I will specify that.]
I don't know to explain this - I've never tried to actually put it into words before - but when I run one or the other pickup, I can hear that the signal seems more...um...wide open or free or perhaps unrestrained; but when using both pickups together, I get a more...um...sort of restricted feel in the signal, which I might describe as a feeling of tension, but which I suppose could be described as feeling tighter or compressed.
I can feel the two pickups merging their signals and in the process, the signal acquires something, and also loses something. The signal, rather than being simply the sum of the parts, seems to be in some way different, more tense. When that happens, I raise the gain on the neck pickup a small amount, to sort of overcome the tension a bit.
I know that's horribly vague and hopefully your electronics gurus won't laugh too hard at my way of describing the feeling instead of speaking in terms of fundamentals, overtones and harmonics. I do consciously avoid over-analyzing the details of tone, as I tend to get focused on the details and lose my more general sense - my engineer side overbalances my artistic side.
Anyway, that is how all of my Alembics have always seemed to me, and it is one of the reasons why I love them so, and why I always run both pickups; that tension in the signal has become something which I just can't do without.