Maybe different categories are not differentiated by color coding the message(or part of it). Instead an icon(maybe colored) might be sufficient. This allows us to use color exclusively to depict ownership of certain game objects to their respective empires.
Off the cuff, that sounds about right.
1) Color code the event icons in a uniform way
2) Color references to empires in the empire color
3) leave everything else white or grey
If it becomes a problem, that too many techs are researched, or too many things are produced, maybe there could be "container messages", that can be uncollapsed to reveal the individual messages. I realize that this is an UI fix for a game design problem, which should be avoided in the first place.
I think if so many techs can under normal circumstances be researched that it is burdensome, then the tech tree probably needs to be pruned.
I could imagine the output of shipyards getting excessive in the sitrep... probably the output of a single shipyard should be in a single message, no matter how many ships that is.
Un-collapse-able messages are likely to be useful at some point, for instance a "Victory at system X" message, might open to reveal a list of ships destroyed on each side.