I understanding wanting more clones, but there's a serious balance factor that can't be supported by just food or even resources that can be indefinitely scaled at cost. The pop-assembly rate is just too damn big as-is. At +9 pop assembly per ancient clone lab on planets under 10 pops, any system that lets you freely sustain more pops gets into a basic pop harvesting issue.
What is your balance to prevent the player from just parking all 5 (or more) ancient clone vats on a world for +45 pop assembly and letting the clones auto-migrate? Especially when all of those pops are getting +25% specialist output modifiers?
Nanites are 'nice', but any resource that you can get indefinite numbers numbers of on the galactic market is not a viable blance. You'd just invest your pops to cover the cost and buy more pops with the profit.
The best I can think of is to provide a way to raise the pop-cap, not the assembly, but even have that limited on a per-planet basis.
Consider a Perfection-unleashed 'Clone Sustainment' building, limit 1 per planet. The building provides +10 clone pop sustainment, but 0 pop assembly. It's literally just there to keep your clones from dying, but you're having a small clone population at best- effectively +10 clone pops per planet you own, and raising your empire limit by 10 per planet conquered. You'd still populate new planets fast, but your existing worlds would still need outside alien pops to be exceptional.
Maybe you then upgrade the sustainment building with cost/strategic resources. Say an either-or substitute of the Bio-Ascension clone vault. The upgrade raises it to 20 pops, letting you have more.
(Though if this is too generous, you can always balance the numbers. Maybe Tier 1 gives you 5 pops- enough for 2 rulers, a district, and a district modifier building- and Tier 2 gives 10. Or whatever.)
The point is, the empire limit of pop can raise on a per-planet basis, but raise slower than what you'd get if you conquered like you're supposed to. Perfect ascension's +40% rulers/25% speciailists might make a 20 pop planet as productive as 25 pops, and be reachable easier, but it'd still have later-game dropoff.