It can't be done in a mod, as it needs engine modifications. But that doesn't really influence the complexity of the problem.
There's an advantage that with the current game, it already keeps the network lag caused by players. So now the host should just calculate some good default from that every x turns (f.e. make sure 90% of the turns fit in the given turn time).
Other games probably do this differently. They could already start the animation before the command is and to the host. So just to provide some user feedback. This would probably give better results visually, but making a distinction between real and virtual commands well be hard.
I do understand the mouse issue now. So I guess it's mainly because your mouse is to precise, and it starts drawing a rectangle to early. I don't have a gaming mouse, and I'm not that fast to move, so I never really make an accidental bounding box.