I rarely mess with the tone controls on my amps. I usually set them for whatever room I happen to play in and they stay in that position. Setting enough low end and treble to fill the room with hi fi tone and then adding or subtracting mids for presence. Even when playing different guitars the tone controls pretty much stay the same on my amps once I find a good balance. I feel that a good amp will make a good guitar sound awesome without much tweaking at all....but only if the amp isn't moved to a different location or even a different angle in the room it's in.. (my disclaimer).
When I did have the Valvetronix I usually left the middle tone knob at about 1:00 on all the models and like you I compensated with the guitar's tone knob when switching to different pickups on the same guitar. You can always back off on treble with the guitar, especially from Strats, so I'd always eq the amp to my skull and the room for nice crisp highs that I like. The reason I eq'd the tones on the Valvetronix amps pretty much straight up was that I wanted to let the amp models play the way they were designed without imparting any other tone mods. To me they sounded good like this. Also remember that reducing the bass tone knob will increase your ability to hear the treble frequencies without having to actually turn the treble up....and vice versa. You can compromise a good tone spot if you experiment with where your bass tone knob is in relation to which pickup you're playing through and then make the treble tone knob bright enough for all pickups.