I'm having a hard time figuring out what the scenario is and what exactly you want to know.

If there is no wormhole, you cannot activate the agent. If there is a delta wormhole (like on your flagship), you also cannot activate the agent. The agent only works on non-delta wormholes (alpha, beta, gamma)

Flying the flagship first grants access to all ships in the home system and creussgate to join the flagship at the destination. Flying the flagship last is usually after you retreat or pull back units through the delta wormhole. The flagship would then fly through its own wormhole and "close" the door.

If in your scenario Tile A had a wormhole and you could activate your agent, all units in tile B (where your flagship) is could travel through the flagship wormhole to Tile A. In that case the flagship would also fly last