Hey Pako -
Regarding your bottom end question, my 100T/410 Neo is no way bottom heavy. And that's normally setting the vintage channel tone at 6-6-5; I'm still not buying that 2-10-2 is flat. I'll just say that when I switch between the vintage and overdrive channel, with the overdrive channel's bass eq set flat, the bottom end matches. And that's with no overdrive, just using the OD channel as an optional eq for a touch of upper-mid boost on songs that need it. But I'm using standard, 4-string, passive basses. G&L L-1000 with flats, Jack Casady Epiphone with rounds.
Plus, I am no way a sub-low freak. I much prefer a punchy mid-bass sound, which the 100T/410 Neo gives me exactly that. So I'm puzzled how you're getting too much low end, while obviously setting your vintage tone for less bass than I do. Where do you set your tweeter level?
Could it be that you are mis-matching technologies? Meaning, could it be that the bass is designed to have extended lows that might be perfect for studio use, but that do not translate well to a 100w tube amp? It could be that an excessive amount of sub-lows are choking down the tube amp, and what is suffering is upper mid and high frequency definition.
Just one man's opinion, so don't start throwing rocks, but by the late 80's I had gotten rid of all of my active basses, as I never liked how they translated onstage, even though they sounded great in the studio. For live, give me a well designed passive single coil anytime.