Take the typical Minor pentatonic Box for example. I learned to play this with fingers 1 - 4 on low E string, then fingers 1 - 3 on A, D, G strings, the back to fingers 1 - 4 for B and high E Strings. Now when I practice, I am intentionally using fingers 1 - 3 on low E string, then fingers 1 -2 on A, D, G strings and fingers 1 -3 for B and high E strings. I think the new way I am making my hand learn will be way more efficient. It already feels much better when I get into a groove but it’s not ingrained yet since I used my pinky for so long. Just thinking out loud today 
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This immediately came to my mind when I read your post:
To my shame, pre CtC Shawn Lane was a name I’d heard but I’d never listened to any of his music and didn’t own his instructional videos. Now that my ignorance has been healed, I try to do as he does to the best of my abilities.
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Cool! I dont have time to watch the whole section now, but it seems like for the position 2, which is the one I was referring to, he used Index - Middle finger on the B string and Index-Ring on everything else?
After a second viewing, I guess it doesnt really matter. The overall point is that for all the pentatonic boxes, he leaves the pinky out regardless which is crazy to me how my hands decided to gravitate towards that when I first learned lol
I hear ya. If I had a nickel for everything I gravitated toward that was not THE BEST way to do them on guitar…I’d have enough nickels for a lifetime subscription to Masters In Mechanics 
Well I actually remember watching that SLane pentatonic video and starting to practice those chunks of 5. But I definitely remember thinking he had really small fingers and wondered why he didn’t use pinky for some of those sequences. Def going to put the video on later and practice to it with his fingerings. Like I said, once the habit becomes a bit more permanent I think it will be more efficient. I probably just have to change the position of my fretting hand a bit.
Gary Moore uses his first and second fingers for much of his 2 notes per string pentatonic playing and he is lightning fast with perfect intonation.
I have tried to do as you are doing (using fingers 1 and 2 on the middle strings). So far, I have not been able to get much speed up because I find the stretch somewhat painful.
I have started to make the change and I like it a lot better. I didn’t know Gary Moore did that I’ll have to find a video!
Check out the following link. Not only will you see Gary’s fingering, but the lick is transcribed for use.
Cheers.
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Wow that’s cool. Im still adapting to the fingerings change, but I gotta say it is more efficient with pentatonic licks