Spent half a day on this and tried everything I could think of. The only real differences are:
1. That the prerequisite tech for 'elite engeers' is a selectable tech, while the research_org1_droid foundry (prerequisite for droid controler) is not, nor is is part of the CIS players list.
2. The droid contoller is not a 'selectable' ability, but rather one that the ship starts with.
Other then these, they are the same, and now matter what I changed, could not get it to work. After so many changes, I grabbed a new copy of the three files in question, and put them back into game info. Now, I cannot get droid controller to work at all. Has anyone else had problems, or is it just me, as with all of my fiddling maybe Iv'e changed somthing else?
Also, all of my testing was done with a save game, working on the assumtion that these changes were save game compatible.
Lastly, if you can get it working, I think from a balance point of view, the timing part is only a very subtle change. I set my stats as only stackable to 2 (was three), range of 14000 (was 12000) and up to 7 targets (was 5). This way, the buff is less powerful (with the three stack, we are talking about 30/sec shield restore AND 60% decrease in weapons cool down) but better spread. Admittedly, these balances are in line with my other modification of 2.5X shield strength and larger gravity wells, among other things.
Sorry I could not be more helpful, but I'm not really well versed in modding this particular game.