OEMizer creates its own folder (based on the name you give it) within the OEM directory. So by using it, you will add your own folder to the 2.03 OEM with all the settings you choose (and also create a nice box for you to check in BuildOS).
This being said, only settings that you specifically define will be altered. You will not change any of "our" settings, but there is possibility they can collide with settings somewhere else.
ie: one oem can't set a registry to 0, and your oem set it to 1. Either buildOS will give you an error building the .hv, or you don't know which one will actually be set.
Ghetto actually worked around this for our settings, so that by selecting "Tweaks - Registry" in BuildOS our settings automatically overwrite any settings set by registry files
This is done by using a provxml. Many folders have them, and they are basically files that add registry settings or modify folders on the initial boot of the phone, as opposed to during buildOS.
This is the same method things like the Carrier folders use, instead of worrying about errors with the registry, they're provxml files that are easily inserted.
That was all really for info, just know that if you try to change something that we already change in the registry tweaks provxml, ours will win
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