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Does anybody else pluck like this?

I call it my "acoustic guitar" method, where I alternate notes of a line with my thumb and hit the rest with my index and middle fingers, like an acoustic guitar player. Playing like that (since I don't have the blessed Steve Harris right hand yet) allows me more confidence, speed and stability in my playing.
 
I do that sometimes when I play chords, or when I'm just lurking behind a melody or something like that.. The reason why I dont play like that when playing groove, is because you don't get the punch from a thumb as you do when playing regular.
I would suggest you learn the "ordinary" way, but don't by any means ignore the technique you are now using, it's beautiful for certain things.
 
If I'm reading you correctly, you're basically referring to "classical guitar"-style picking?

If so, I employ every now and again. I have actually found it quite useful to pluck more controlled root-octave notes successively when moving up and down the neck, ala 70s funk. By keeping the palm positioned close to the strings, I'll pluck the root with my thumb (not slap - just pluck) and then pluck the octave with my index finger.

When you are playing root/octaves in relatively quick succession, it's easy to get a little out of control by plucking both with the index and/or middle finger, thus the need for more steadiness and control. This method helps me, at least.

Pick up the Car Wash soundtrack and practice along.