But are these different from individual ships jumping? If so they are hard to distinguish. At least for me.
Actually I don't think individual ships jumping spam you with those messages? I haven't noticed anyway, the only time I seem to hear the messages is when my actual fleet jumps. I'll try to pay more attention

That is correct. It makes no sense to hide them behind the names when the star names option is on.
Ah, I misunderstood a bit. Yeah it's kinda strange that the names hide the box, but you still have to hover over it to see the exact breakdown of structures one way or the other. It is nice to get the general idea by the pip marks in the box, though. This bothered me too at first, suppose I just got used to it

Would be nice if the position of the names could be adjusted a bit.
It seems like to me at least that fighters don’t get called back until there home ship hits the end of the gravity well. When the fighters do get back to there home ships the ships are so close to each other that the fighters kind of bounce off one another keeping them from docking with there home ship. A trick that I use to get around this is to move my ships as group to jump point and when they stall out I unclick then re-click the move as group button. This gets almost all my ships to jump at the same time except the two or three ships that had docking issues with there fighters. The fighters are then able to dock and their parent ships soon jumps afterwards.
I think what Ron meant, and this is what I see whenever I look at a jumping fleet, is that a carrier doesn't actually wait for the squadron to return to the ship. Sova is usually my flagship and I don't think I've ever seen it wait to scoop the squadrons before jump, even if they're half way across the grav well the ship'll jump, the squadrons will disappear off the map and will be in the ship's hangar when it finishes the jump. I've experienced the stalling when jumping a bit, but I don't think that has to do with fighters, I think it's trying to put each ship in a precise spot before it can jump, and it's the ships bumping each other that slow it down.
Tonight/tomorrow I'll try ordering my squads to the opposite end of the grav well and then jump the Sova out and see if it waits or no, to do a more controlled experiment rather than casual observation