I don't think it's just interfering with WriteMakefile, but instead either other XS loading or file writing.
In the dist in question, I have a bunch of tests that read/write to sqlite databases using DBD::SQLite. I commented out the APR load in Makefile.PL to get a complete Makefile. Then I started running the tests.
All of the sqlite tests were failing with strange errors, corrupt db, locked db, full db, etc. In my core module, Handel.pm, I commented out the same APR::UUID eval statement I use in Makefile.PL to find the appropriate uuid module.
As soon as I commented out APR::UUID, all of my sqlite tests passed. If I uncomment it, they fail again.
So, it's not just EU::MM being borked, but other things as well. I don't know enough to know whether it's effecting the loading of XS in other modules, or some read/write process being borked.