'El Hombre' is a single one only choice, but remains in play for the whole game and shifts between units at the player's discretion. It can only effect one unit per phase though.
The Militia have it rough mostly and the idea is that for a brief period of time a unit will actually obey an order straight off the bat and with no discussion... making it at the player's discretion is throwing him a bone. You could try it out with your opponent choosing which unit it will be though, could be interesting.
The * choice refers to each type, not an overall either/or. So you could have a single FT-17, 'El Hombre' and either Fanatic/Hardened/Motivated Milicianos in the same force for example.
Discounting 'El Hombre' and the troop quality aspects, material was initially in short supply, hence the restrictions.
Hope that helps.