Hooks for own tools during Quartus Compilation?

You could create an Avalon mapped component that instantiates a ROM. You will get a hex/mif file to pre-initialize it which you can inject your version control number into (script it or manual). Then parameterize the memory to be LE based instead of memory. By using LEs it should synthesize into wires and be almost free (you'll have a little bit of switch fabric logic created).

You could also get really fancy and avoid the memory instantiation altogether and just have a script that parses HDL and modifies a parameter within it.

I hope that helps, maybe someone else will have a better idea for you.