I want to add an additional configuration to the out of the box Enterprise Wiki site definition. Should I adjust the OOB site definition itself, or is there some way to staple it to the definition without touching the OOB files?
You should not change the OOB files for several reasons:
If you want to make changes to what happens when a user creates an Enterprise wiki site, the you should make a feature which makes the changes needed and then use Feature Stapling to add that feature to Enterprise Wiki (ENTERWIKI#0).
If you want to create a completely new Configuration, then you need to develop your own site definition where you copy everything you want from the Enterprise wiki onet.xml. See How to: Create a Custom Site Definition and Configuration