edit: Fixed in the latest version. "Autoplace Optimized", the default mode, doesn't guarantee ore patch coverage but it usually happens. The other mode, "Autoplace", does guarantee trees over ore patches.
Yes, unfortunately no amount of noise boosting seems to override the vanilla tree removal for resource patches, and doing it post generation slows things down a ton.
I could possibly do something like that with big warning signs that it's a huge performance hit. Well, anyways, glad you found a workaround.