I can't possibly imagine how you're going to carry off local samescreen co-op game with RTS elements in an open world. Without channelling objectives (as in levels) you're only inviting frustration.
I guess we can get a few pointers form the Protoss.
Their structures and units are produced off-map on their homeworld and teleported onto the battlefield when needed. In the same way, you can have a base elsewhere. I don't think it's all that necessary having to click on a building to procude units - a menu would do. The units would then arrive from off-screen. To prevent it from being broken, this could be done in specific checkpoints (bonfires?) or just dissalowed in specific locations (like you can call reinforcements in the overworld, but not deep within a dungeon or with the restriction that your forces would appear at the location's entrance).
The main bases themselves would exist on the world map - you can visit them but it's not necessary.
There could be a local and global resource count/bank, so you don't have to start from scratch with each quest/mission.
The thing is - which is better for that kind of game?
To have an open world in which you can discover objectives (like in Metroidvanias or the Elder Scrolls)
-or-
to have a more episodic-like structure that follows a campaign? (like in StarCraft or Devil May Cry)
What are the implications of choosing one over the other?