I too expected a reuse of the full name when I first clicked...

"Master Control Program" was an operating system for Burroughs mainframes in the 1960s and 70s. That is probably where Tron got the name.

In the '90s, I used another "MCP" on the Amiga: it was a "commodity" that tweaked and patched things, similar to PowerToys on MS-Windows. And I think the author has said that he got the name from Tron.