Hey thanks!
I'm afraid your carrier idea is likely impossible, there are no pausing commands for animations, and generally they all act simultaneously on the part. You could get one to run off and up a straight runway, but it would then reverse backwards back into place...
The closest I ever did with this sort of idea was housing fighters in a carrier, and having doors to reveal them, its in this set, I think around minute 2:
As for your question about the merged squad and battles... well, they are not going to scale perfectly, but I use small black parts on my models, offset, to ensure a certain scale in galaxy map and then I eyeball the various scales between units. Mostly, this is a matter of making Tiny ships at about half the normal size, and then everything scales mostly well from there. In the battle-viewer, (I almost never have time to actually play lol) I have no idea if they scale correctly, but I think they do, as I'd be surprised if they didn't just apply the same scaling in the galaxy map.