I only have 1.5 years experience with bass, and only practicing 1-2 times a week at best.
When I started, I also instinctively gravitated to playing all notes with the index. It was much easier to play correct timing and keeping consistent volumes. But it was also immediately clear to me that in any song with 16ths rhythms I was tensed and getting tired before the song was over. It did not take more than just a bunch of practice sessions with basic repetitive exercises, in order to get used to alternating index and middle, at least on a single string (I still mess up the alternation when there are lots of strings changes) so at least I can say it is worth trying it out to be able to get more relaxed.
Personally, I find it interesting to compare this question to the analogous one with respect to pickstyle: i.e., downstrokes-only vs. strict alternation.
When I started out I focused entirely on fingerstyle using the traditional (alternating) two-finger method, so that became natural for me and I rarely deviate from it. When I decided many years later to learn pickstyle, the analogous technique of alternate picking came naturally to me for more-or-less the same reasons, in particular efficiency.
But when thinking about it I also discovered an important difference. One reason I enjoy playing with a pick is the physical up-and-down motion in the wrist -- like a rhythm guitarist, so to speak -- and as much as possible I like to play downstrokes on downbeats and upstrokes on upbeats. When playing straight fours or straight eights, etc. this is the same as strict alternation, but when the line doesn't follow that rhythmic pattern I tend to go with the downstrokes-on-downbeats rather than strict alternation. I suppose technically this would be like using your index finger on downbeats and middle finger on upbeats (or vice-versa), but to me it doesn't feel the same. When I tried to play fingerstyle using the index-for-downbeats method it just didn't work for me in the same way as the downstrokes-on-downbeats method does with a pick, so I still tend to strictly alternate with my fingers independent of the upbeat/downbeat distinction.
Does that make sense?
I think yours is a very keen observation.
When I started studying electric guitar about 30 years ago, my first teacher immediately taught me both rhythm and soloing, but as a bluesman and "vintage rocker" he wasn't particularly obsessed with technique or efficiency, his main purpose was to teach me to sound good, so not much attention was given to exactly the direction of the picking except when it mattered to deliver a better sound, for example when playing reggae (lots of upstrokes) or funky (downstrokes and upstrokes chosen precisely at different spots).
A few years later however, I moved to under another teacher who was into heavy metal, and definitely obsessed with technique. He saw that I was over-reliant on downstrokes on non-chords stuff, and he corrected my technique with a set of exercises in strict alternate picking (plus some "against-the-grain" exercises when I had to force myself playing everything with upstrokes just for the sake of rehabilitating my weakest side). Once you get used to alternate picking, it gives you a strong sence of reliability, to the point that your right hand will "ghost" the alternating movements even when you don't have a note to play, so that it remains synchronized with the beat. I think this is exactly what you are talking about when you say downstrokes-on-downbeats, except that more generally the right hand is synced with 8ths or 16ths or 32nds or 64ths depending on the speed.
By the way, in the world of guitars, alternate picking is not even considered the most efficient but rather the most reliable; sweep picking (basically raking in both directions) is considered even more efficient in terms of economy of motion, but is a lot more variable so it requires more thinking, while once used to alternate picking you can almost switch your brain off and let the right hand work on autopilot
