Unfortunately, yeah, I think the updates wipe your mods. Also, I think the modder-friendly was more geared towards making it easier to create mods, not necessarily making them easier for consumers to use.
The update makes changes to the game's resources; in order to make those changes, it also needs to make sure those resources are uncompromised.
It shouldn't be deleting your override folder, so anything that's in there should still be preserved. Any mod that doesn't drop the changed file into the override folder, though, is probably going to be undone by the patch. (that's just the way patches work, unfortunately.)
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It shouldn't be deleting your override folder, so anything that's in there should still be preserved. Any mod that doesn't drop the changed file into the override folder, though, is probably going to be undone by the patch. (that's just the way patches work, unfortunately.)