Umm... I guess I'll finally say something, considering that I've been amused that nobody else has figured this out.
There
is, in fact, a consistent way to guarantee your .rgu file gets resolved last.
And the way is...
...It's all alphabetical.
I have my own customizations in an OEM labelled "ZZZ Customizations ZZZ". Always goes last. You can look at the CreateOS.exe log when it's reading the .rgu files, and you'll notice that the last alphabetical folder is the last .rgu read.
I was going to wait until the forum ROM project had gotten underway before mentioning this, but if people are going to need to go through this much trouble to try and get around this, I might as well pipe up now.