I won't get into the double-bass position thing like @SteveCS (I play double bass but there are multiple "position schemes" taught, and they don't help me) because bass guitar is a somewhat different animal.
Your example above involves "microshifts" or "pivots" no matter how you play that A major scale, so the "pentatonic box" doesn't apply perfectly. Playing the low A with your middle finger means a stretch to get the next note (B) with your pinky. I'd be more inclined to use index finger on A if my next note is B (unless it's B on the A string, in which case my pinky would fret the A!). BUT ... if playing a triad, where the next note is C#, I'd use the second finger for the A.
The real point I'm making is that fingering choices should answer the question: Where am I going next, and what's the easiest way to get there? Any finger works on any note if you take it out of that context.
I was with you until you approached the end of that statement. Why and how would your second finger be "conceptually" - or otherwise - the root of the position if you're playing octaves or fifths up? We like being able to stay in one position, but we better not depend on it. Shifting is part of the game.