Could it be made so that the map generator places N advanced factories together on the same planet, where N is the number of players, and then the game distributes them automatically on planet capture? It would make it more clear to the players, and I think it's more elegant than spawning them when the planet is taken over.
Problem is, then you are hosed if you add or remove players later. And it will not work with existing saves. In the current model, it will give one per player at the time of capture. If one player later joins, then they lose out on any past captures, but can take advantage of any future ones.
I understand concerns about new factories suddenly materialising beside existing ones: it'll just look and feel
odd (accepting fully that it is ultimately a helpful multiplayer mechanic to be able to have a factory each). Notwithstanding that this is the easiest solution there must be a better way... somewhere; even if it's only aesthetic, i.e., stacked on top of each other with some form of clever click algorithm to bring the owners’ factory into focus first. Between the gifting system, pre-populating the map with factories equal to the number of starting players[1] and this solution, to my mind this solution is the least graceful. Sorry, but it is.
I know this is largely an aesthetic issue, and perhaps a logical one as well, but how about approaching this from a slightly different appearance perspective: Keep the central factory as it is but once captured instead of spawning copies of itself it extends a ‘production control module’ beside it for each player. (These smaller modules could appear to be on the end of a long, gantry-like armature so multiple modules form a radial pattern around the central factory graphic[2].) Each module then acts as the primary point of interaction for the player and the central advanced factory sprite in effect becomes a hub-like placeholder, i.e., purely for visual effect and has no other mechanical function. Once captured this gives the impression that the factory is somehow unfurling and making itself ready for multiple concurrent manufacture runs, just as an advanced facility might do.
Personally, I didn't mind all the gifting that used to happen. In many ways it encouraged team play (you had to prioritise output) and interaction, and it gave a stronger sense that you're all in this morass together... *shrugs*
[1] And if the number of players did increase everyone would fall back to the gifting method anyway.
[2] Gone are the days of doing speculative PNGs for this stuff now. 2D pixel stuff was a doddle to kick out at a frightening rate but 3D stuff takes a while to look white-hot (and why would you not make it look white-hot with no poly count limitations), too long for me these days. (Even tho a few years ago I spent large chunks of my life inside 3DMAX and Maya for other indie projects.)