I don't really like the idea of player fleets and AI fleets following radically different rules. Makes everything feel overly "gamey" and arbitrary. =/
I get what you're saying, but don't agree in this particular case. They play by the same rules regarding EB, and whether their supplies cost them money or not (or even exist) is something of a moot point, since it's not directly visible to the player. The feel of it could be enhanced by tweaks to the EB-usage AI, perhaps. To further support that: consider that EB usually gets singled out here, even though AI fleet CR recovery works the same way regarding supplies.
But, anyway: I see your point, but imo it's "minor" rather than "radical",
in terms of same-rule-following. That's what gets blamed, but that's not what the actual issue is. It's not even clear that following the same rules would help with AI EB use - if they were to be using supplies and restocking, that's very much the same situation as now, anyway.
Edit: And it's very likely to lead to other issues. Basically, the idea is "let's assume that other fleet commanders are competent at managing their supplies instead of simulating that directly". Simulating it directly, best-case, will eat more CPU and result in similar behavior to now. Worst-case, they won't be competent at it and there'll be abusable issues.
A visible nod to them using supplies - such as, perhaps, fleets occasionally acting as if they're out of supplies - would be imo all that's necessary to fully "sell" it here.