Agh, my bad, I forgot about those... Well, for starters, there are some things that are already quite suboptimal in vanilla: The upper left is reserved for system messages. There are so many things that could be fixed that I don't even know where to start, but to keep it simple right now, I would place those tech icons lower, at the same level as the group icons on the left, and with the same separation. Then you would have space for your notifications.

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You don't have these tech research progress indicators ?

How would it look exactly with deactivated unit colouring? I wonder if that would become too noticeable. An alternative I proposed is that "the enemy would see as its own", but of course not control, and it could be attacked as any enemy. Regarding "sounds more like scouting and less than spying", limited speed and FOV would solve that, with a larger FOV reserved only for Heroes (from gossip and such).