I agree with Proleric. There’s no benefit to module content taking precedence over hak content that I can see. And there are several serious problems with it.
Patch hak-ing developed (at least as I remember it, and this is why I adopted it) because it was the only real way to “patch” a running game. All of the module resources are copied into the first savegame, and without a patch hak, that version of the module is fixed thereafter as the one the player is playing. If a player found a bug halfway into a playthrough, you could address it by putting the fix into a patch hak for them to download. Otherwise, they would have to start the game over again from scratch.
Gradually, and as I came to use the approach more and more over the course of a decade, I found that it came to make more sense to just build resources in one module, and then share them into another via the hak. The remake of Sanctum 2 is full of examples of this: things that I had re-done in the remake of Sanctum 1, and then just found it easier and more convenient to add to the (shared) haks to use them in Sanctum 2.
It’s also how I made it possible for players with an ending savegame from the first module to simply load it (with the updated haks) and launch the sequel, even if they’d saved that game years ago, rather than forcing them to do another whole playthrough. This is also how I planned to make the same thing possible for players of Sanctum 3 (if and when I get time to finish it) for people who want to use an old saved game from Chapter 2.
I shudder to think of how many weeks or months it would take me to restore my modules to working order if this change isn’t reversed. I’m not sure if people who haven’t used and relied on this technique fully understand how useful and powerful it can be, and how much it can speed module development and testing, but I definitely think that it does.
Regarding a switch: as long as the switch’s default is consistent with how it’s always worked, and as long as the switch is set in the module and not by the player, I don’t see a problem with it. Otherwise, many (my guess would be scores or hundreds) of modules whose authors aren’t around to maintain them any longer will cease to work. NWN:EE was developed and released on the premise that backward compatibility was one of its fundamental principles. A change like this, if it stands, would be a major default on that commitment.
Just for the record, I’ve found the opposite to be the case. Scripts are one of the things I rely on most, and find it easiest, to put in haks.