I depends... :-).

I'm in a similar situation and considered this very question a couple of years ago. I like both of my guitars for different reasons and each has a slightly different feel. I didn't want to become fully comfortable with only a single guitar. Bends, palm muting, pinch harmonics...these all are executed slightly differently on each guitar. You might wonder about bends, but I have a maple fretboard on my strat and rosewood on my LP - different feel under the fingers between them. Also different scale lengths, which means different string tension, which means more/less force to bend between them.

So...if I'm in a mode where I'm working on a lot of theory, scale shapes, chord shapes, I'll switch off once a day. If I'm learning a song, I'll choose whichver guitar fits the desired tone the best. Once I've learned the song, I'll play it on the other guitar just to see what it will sound like and also develop some flexibility in switching. If applicable, I'll throw my acoustic into the mix as well.

When I was playing in a band for a couple of months, I used my strat exclusively since I was using that guitar to play out. There, comfort and familiarity with the guitar was important.

This all may seem silly, but when I first got my faded LP a couple of years ago, I noticed a big difference between the 2 guitars. Since I've been switching back and forth , I find I don't really notice much. Guess my switching worked :-).

So I think you are smart to do this. From doing it myself, I find now it doesn't really matter much, which is where you ultimately want to be.