I am looking at pictures of Cilia on Google right now, and I noticed that in all of them Cilia is always located around the whole membrane, not just in patches. I was thinking that maybe we could have cilia be an upgradeable feature of the membrane? For example, you could upgrade it to create a cell wall or add cilia (which could be upgradeable further to create a higher density). I really think that we need to stay away from external organelles until we get internal ones working perfectly, but this is just my opinion. As for agent secretors, I was thinking that they could be internal organelles that have to be located on a hexagon that borders the cell membrane (which could easily be checked by seeing if a hexagon has less than 6 neighbors).
Sorry if what I said was confusing, but what I meant was that the player places the flagellum as you described, on edges of the hexagon, and afterwards they are repurposed to the closest point on the generated membrane.
Final question, why does the player first put down cytoplasm and only later the actual organelles? And if we are going to allow for empty cytoplasm hexes, how should this factor into the dynamic membrane? Should they be treated as invisible organelles, or should I just ignore them for my generation algorithm?