"Flat" on an instrument can be a slippery critter to get hold of. To me, "flat" means no EQ applied to the output. Since nearly every preamp (separate or built into an amp head) has some sort of coloration bias due to the designers' intent, determining how your bass sounds with NO EQ can be tricky.
I listen to my instruments through some good AKG studio headphones and a decent mixing board, interested to know and remember the basic sound of all of my basses with their controls making the least change in the tone.
Having that sound in mind, I can find something close to it for any given amp or DI situation, and can more quickly and accurately EQ things as desired from my instrument's knobs and my fingers. Yeah, it's also in the ears, not just the fingers, IMHO.
That said, since this question is posted in Basses, here are my humble opinions on "flat" vis a vis instrument knob settings:
On a passive Fender, all tone controls are cut-only, thus tone all the way up and all pickups on full is "flat" on a passive Fender (to me).
I've always felt lowering the volume of a P-bass pickup changes its tone slightly. The blend/mix of Jazz pickups is obviously going to change the tone.
On a Sadowsky pre-amp equipped bass, the preamp has it's own EQ voice. The treble and bass knobs are boost-only on top of that voice, and the "Vintage Tone Control" (VTC) is cut-only for everything. "Flat" is therefore the pre-amp boost on zero, and the VTC open all the way, i.e., no boost and no cut.
Many other on-board preamps offer both cut and boost, so having "flat" in your head for a given instrument will be affected by that as well as onboard preamp voicing/blend at the detent (center) setting.
Furthermore, on-board preamps often offer trim pots or band switches for midrange emphasis, and other features making "flat" on the instrument pretty meaningless.
All IMHO.
