I know this isn't how you're supposed to use them and that in this context what I want to do can be resolved by DefaultWindowX/Y=50%, but we were joking about horrible ways to do thing (jokes like !ToggleMeter #CurrentSection#) and all of that and I discovered that having section variables in the Default Settings actually crashes Rainmeter AND because it's not even able to load past the settings, it will always crash and not write the skin to rainmeter.ini
Thanks for the bug report. This has been fixed for the next version.
The actual problem was using the section variable parameter like :W, since it would look for the "skin" and "section" to get the value. In this case, there was no skin which caused Rainmeter to crash.