I must aggressively disagree. It should not be automatic, it should require player interaction, as the flag system does. I have activated many ships just to use them briefly for one reason or another, and then abandoned them when I no longer needed them, and I don't want to be stuck looking at every ship I ever touched forever. A system where I can pick and chose which ships I can see and which ones I don't is much better. This is even more true in multi player. All someone would have to do is touch my ship's cockpit one time and they'd be able to track my movements forever and maybe I don't want that. Flagging is better for this because if someone put a flag on my ship to track me, I could find and remove it.
If you lost your ship before the flag system was created (as I did mine), I'm sorry to hear that. Get a new ship and rebuild; I've done it multiple times. I currently have 3 ships in my single player world (about to be 4) and I know where each one is because they have flags (or are parked near one). Now if someone forgot to place a flag, I'm sorry if this sounds harsh, but the system didn't fail; that person did. The devs provided a solution for this problem, it's not their fault if some players fail to make use of it.
The system you are describing already exists exactly as you describe it. The flag is just the on/off switch for that system. All you are doing is asking them to remove the off switch and I like the off switch.
Even if they do create a ship beacon system like this, odds are you will have to interact with you ship again to set it up so you still wont get your old ship back because how does the system know which ship you want to be bound to? You have to tell it "this one". as mentioned, I've touched many ships. The system would have no idea which one I want to bind to.
As for teleporting to a cockpit someone else placed in multiplayer even if you never touched it, that's obviously a bug a warrants a bug report. No way that's intended.