The filter does not remove frequencies above the cutoff setting - it just rolls them off at some fixed slope (12 dB per octave for the low pass on the instrument, I think). Meanwhile, a typical shelving tone control (ignoring the slope where it kicks in) cuts or boost everything above/below some fixed point, by a fixed number of dB, often by a max of about 8-10 dB or so.
So you just take the two curves, for the filter and tone control effects, and for any given frequency, add up the two values to figure out what the resulting output will be. The order doesn't matter.
Now... I will grant that in reality, you may hear some differences if you take a signal that is already down 24 dB, and try to boost it by 8 dB (for example), rather than boosting it first and then rolling it off with the filter. But this is only relevant if noise/distortion/low signal losses/etc. are creeping into the picture. And in practical terms for these instruments, the filter slope is really only relevant for a very small number of octaves anyway, so we aren't losing that much. We discussed this in the process of designing the circuit for my custom, and the bass/treble pots are the very last thing before the output jack.
It may also be worth noting that this is really only relevant for a treble control anyway, given that the usual bass control will operate well below the lowest cutoff frequency of the filter. And in the treble region, the sharp Q spike you can get with the filter is likely to dominate your tone anyway (though again, a treble control will still raise or lower that and everything around it).
I'm not quite sure I understand the comment, because the output is mono. That isn't what determines whether the effects are simply additive. However, in practical design terms, it is certainly simpler to apply bass/treble switches or pots, after summing the output from the two pickups and possibly filters. This way you only have one signal to modify, though of course if you wanted separate bass/treble controls for each pickup, you would need extra circuitry and could it before or after the filters.
Why is there tape on the trim pots???