So What ? - The Disapperaing of any POP on any Tile is just like the Bombing of any World, in Which You simply kill some POPs - Are there any Problems ? - No !
You seem to be confusing technical possibility with balance implications.
Just because the rare case (how often does a pop get killed by bombing in a day, vs how often are pop's subject to monthly growth in a day?) implicates the engine can handle it, doesn't change a thing about the facts I mentioned earlier, regarding how many balance issues it would bring to make a core ressource, upon which's logarythmic growth the entire game concept bases on, instead grow regressively.
So, you're fine with the logic that a single ship should be significantly stronger then the same ship in another empire, solely because the other empire has more instances of that ship.
(And don't even dare to mention 'maybe they have better tech', because that's a completely different factor in first place.)
The Thing is, that You can even adjust the Amount of Empires at the Start of the Game + in the Progress of the Game, the Amount of Empires will naturally rise and fall + You don't consider Empires, Which are simply in an Overlord-Vassal-/ or Overlord-Protectorate-Relation ...
And all those variying numbers are supposedly considered in the default generation sequence, which populates the galaxy based upon number of starting empires, number of habitable worlds (by %), etcetcetc.
Being able to tweak these values because it was a frequently-requested feature does NOT mean anything in context to the developers original intention.
By that logic, you could claim that the developers wants us to always play with 16 ethics, because it's possible to add that with mods, because the devs implemented hooks and functions to mod these features.
From experience as a developer, I can tell you that the decision to make things configurable or moddable, is because too many people disagree with your (developer) vision of the game and the only way to keep them interested is not by forcing them to play 'your rules' but by allowing them to modify the rules to their liking.
It's naturally to scale the Core-System-Cap in Regards of the Galaxy-Size ...
Unless, of course, you have some elaborate reason that might imply otherwise, which is not solely based upon your own preferences and oppinion.