Echo may enjoy this one.
So the FPS players will get some sort of FPS economy in the far far future, probably after 1.0
But what about the Commanders? Well if they did get a personal economy and if they did get Commander abilities then I think their personal economy could fund these abilities.
Lore justification? Space based assets that provide the artillery fire. Why do the humans not destroy the other humans' orbiting artillery platforms? Suppose Sol and Centauri have a treaty limiting the scope of engagement with each other. Idk how else do we justify it? As long as we get space based artillery I think we are covered for a lot of commander abilities.
What kind of commander abilities should there be? Well I would group the abilities into 3 categories. Support, Intel, and Offensive.
Support provides support to players and AI on the ground. So suppose Alien commander could fund a sudden mist field to cover the advance of the alien army, for example. Human commander could provide enhanced enhanced battlefield info, so all units in an area get improved info on enemy locations, path of travel, and where they are aiming. AI could benefit by getting improved aim from this ability while the FPS get HUD temporary HUD augmentations that provide the previously listed info.
Intel would be a Commander trying to learn something about the enemy team. So pay a chunk of personal eco and maybe you could spy on an area of enemy map or you could learn the strength of the enemy economy like number of Harvesters/Foragers or the real time amount of money the enemy team has. Tells Commander what the enemy team tech level is. Each is temporary though.
Offensive would be damage dealing abilities. Think Helldivers red stratagems for example. Calling in artillery barrages, orbital precision strikes, orbital lasers, etc.