As well as posting about the ghostly writing etched into the inside of the hold here, I also put a post on CanalWorld to see if anyone could shed any light on it. And I had a reply from the estimable Steve Priest, who said:
Harland and Wolff would paint reference marks on plates as they were cut and prepared, so that the platers would know which plate went where as they plated the boats up.
They quite often come to light when boats are stripped back to bare metal, and are normally quite easy to read, but I've not seen any cause pitting like that before.
I would think that MS + P means plate M, starboard and port.
Which is very gratifying.