Oh, it doesn't help at all unfortunately. They still get dumb stuck. I didn't explain it very well.
I'll try to break it down a bit more so you understand my opening moves....
1. Build fighter production facilities on HQ and carrier
2. Set rally point for both about 4-5 km away from both at central location between them
3. Typically build the following at each: 4 Hellcats, 4 Bearcats, 4 Excaliburs
4. Eventually, I'll have enough fighters to organize them in a formation. Which requires them to move. Now, they haven't really done anything save fly to the rally point but sometimes it's clear some of them are running out of fuel because they'll start back towards the carrier or HQ. This is where I meant I selected them and tried to force them to dock. Sometimes, they do, sometimes not.
5. If I order the group to move away, more fighters will drop out over time and move back towards the carrier and HQ. Some will dock, others will just sort of sit pretty around them.
6. I've tried building a Confederation dreadnought at times and using it as the forward base. Sometimes fighters will dock with it but I've noticed a lot of times fighters will try to get back to the HQ or Yorktown carrier. That's why I asked earlier if fighters might be tied to their base of creation.