#1
I have my electric in C standard right now but I still think of it in E sometimes. Is that really a bad thing? Like when I play certain harmonic minors for example. I love the way the A harmonic sounds but in C standard tuning it would technically be an F harmonic minor.

But yeah is that a bad habit or does it even matter?
#2
It depends...I don't think it's a bad habit as long as you can be aware of the fact that you are playing in another key. Essentially you're playing a transposing instrument now, the guitar actually already is one, but one that transposes at something other than the octave. It's okay to think of your F harmonic minor as A harmonic as long as you understand that it is in fact, still F.
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#3
it doesn't matter, as long as you actually know what you're doing