OK, that's a good reason to switch fingering.
My suggestion would be to just force yourself to play power chords this new way. It may feel awkward now, but before you know it, it will feel natural.
I've experienced this with the open G chord. I learned a song that required I play the G with my middle, ring, and pinky fingers rather than index, middle, and index fingers. That was incredibly awkward at first. After a few weeks, I could fret the chord either way comfortably.
Just keep doing it and it will eventually feel totally natural.