For #1, that is correct -- cleanup drones and repair drones are considered as part of the engineer superclass. Same as space docks, silos, starship constructors, and mobile builders are all just part of the constructor superclass.
For #2, those are just for you to capture -- enemies never do use them. The reason I made those a capturable thing (way back in July-ish of 2009) was so that new players would actually stumble onto missile silos on occasion and then see that they could use them. Same as the AI does not use its starship constructors, advanced factories, etc, those are all just capturables.
For #3, most likely that is caused by some sort of minor faction -- devourers, dyson spheres, etc, can trigger the on alert -- on alert, now that we have minor factions, doesn't necessarily mean that the AI is alerted to
you.
The Trade ships, which are allied to everyone, don't trigger the AI alert.
Also, regarding the threat going up consistently because of the resistance fighters, the 3.017 update should resolve that. But, please do let us know if not.