"Rolex said the watch is genuine, needs polishing and lubrication."
An 'official' rolex repair shop never saw a used rolex watch that did not need "polishing and lubrication."
...even if it just came out of another shop after polishing and lubrication.
If you like it, keep it. It is a good looking watch.
Maybe buy a used genuine AK dial and hands later to go with it so if you decide to sell it you will have all the genuine parts, this helps a lot even if they are not on the watch. The dial and hands do not need to be in very good condition, just genuine and not refinished.
"Turns out that Rolex thinks the 5500s never came with the Explorer dial."
They think they know it all.
I have a 1002 (1964, cal 1560) with Yuki explorer dial/hands...they did not make a 1002 like that for sure. Ha!
If you keep it, get it serviced by someone you trust, not a rwc repair facility. No telling how much they might charge or what you would get back after they work on it. They can quickly turn your $2000 watch into a $1200 watch while charging you $1000 at the same time.
Figure on cleaning/oiling, new mainspring, gaskets, and maybe a rotor axle...plus case tube, crown, and crystal if needed. Hopefully the reversers are Ok, they usually are.