I understand why you'd say that. I ran dual-source rigs for a long time, mostly as a way of compensating for various weaknesses, and it was a PITA.
But OP seems to have a pretty specific need: have an acoustic guitar most of the time that he/she can overdrive when needed. There's no reason that you couldn't run one pickup through a drive pedal and accomplish that. You could even have a pretty good acoustic sound out of the pickup combination and then just distort/effect one part of it.
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