LQP as documented says to profile the amp with all the eq flat and the amp gain at max.
To be complete, the manual does not say to profile at eq flat and gain max.
This is merely a recommendation for a more authentic over-all LQP.
You can still make a LQP at your desired sweet spot, and it will sound authentic in that very setting, just like a regular Profile.
Only deviating far away from that sweet spot might induce more inaccuracies due to the reasons mentioned in the manual.
If you set the bass knob at "2" for profiling and mirror it to "2" in the Profiler, deviations of the potentiometers taper or even the printed scale on your amp can cause a small error. While the unaltered Profile is spot on, you might experience a larger deviation, when you turn the bass knob on your amp and the Profiler to "10" for an A/B comparison. The small error might get large when deviating by most of the scale.
Once your target amp is well mic'ed and warmed up, it might be a good advice to make that "most accurate setting" LQP, as well as two or three sweet spot LQP's (including the mandatory mirroring of the sweet spot settings in the Profiler), and keeping all of them.
Then they can be compared against each other the next day, and they might all work perfectly and equally, at any settings.