Is there some other way of seeing what you need to see ? I would've thought there would be a simpler way (like having the Makefile.PL print them out and/or assign them to variables for later use) ... though I can't really get my head around your precise requirements.
If you really do need to run WriteMakefile() a second time, would you be better off running it in a second Makefile.PL ? (No idea whether that's a feasible option :-)