Oh sure, acoustic will always sound better, especially unplugged.This suggestion was just for when you'd already be using the electric. 

Though… why not mount a nice piezo to your acoustic, so you can run it through effects when needed but still get a clean acoustic tone? That way you don't have to bother with switching instruments.

In fact, I was curious, so here's your first electric riff match-EQed to the first acoustic riff:

Logic MP3: https://www.dropbox.com/s/ghsqfh9etpepk9a/logic.mp3?dl=0

The resultant curve: https://www.dropbox.com/s/o4p25md0q27zc96/logic.png?dl=0 

Pro-Q 3 MP3: https://www.dropbox.com/s/qotgjjjw9nc1r9u/pro-q.mp3?dl=0

Curve: https://www.dropbox.com/s/h7dj544ltumc6qg/pro-q.png?dl=0

You might experiment with a match EQ plugin. You record the same riff on both, and it will spit out a complex EQ curve to approximately match the acoustic’s tonality on electric. (There will probably be a pretty extreme treble boost.) I’ve gotten surprisingly good results making a piezo sound like a mic, using both FabFilter Pro-Q and Logic Pro’s stock one (but there are others). Granted a full electric with magnetic pickup may be less convincing, but it’s worth a shot.