I think the proposed solution for battle screen timeout is excellent considering all the varied demands of the player base.
I'm not quite so sure about the port battle log off issue. I do agree with Tiedemann that the defenders home port re-spawn advantage needs nerfed if you implement a 30 PB ban after log in.
Perhaps you could have a coincidental mechanic allowing the tagged PB fleet to exit directly into the PB "IF THEY WIN" the screening fight.
IOW - 25 ships log in far enough off to reach the port as PB starts - they are tagged by screen fleet - in 12 min they are able to beat the screen fleet well enough to escape - they can escape directly into the PB but the PB timer now has 12 min run off (the run off could be limited to 1/2 hour to limit this nerf).
Rewards the PB fleet for quickly defeating the screening fleet, rewards the screening fleet for delaying the PB fleet, but precludes endless spawn attacks - the PB fleet only has to fight it's way through the one screening fleet to get a PB.
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The flag system could also have been made to work .............Just needed a limit on false flags and to be mixed in with the hostility generation system.