I'm creating a modpack using Minecraft 1.16.5 and Pam's HarvestCraft 2 - Crops version 1.16.3-1.0.2.

My [instance]/config/pamhc2crops.toml file looks like this: https://pastebin.com/Hu9fwyd1
However, when I boot up a new instance, these logs are generated: https://pastebin.com/F4mrTHu0

From what I can tell, when a new world is created, Forge checks to see if [instance]/saves/[save]/serverconfig/pamhc2crops.toml exists and if it doesn't, it generates the file using default values. And there doesn't seem to be an inherent carrying over of the config file from the [instance]/config directory, so this will always be the case. Accordingly, this means that none of the changes I make in the config file matter.

I know that Minecraft version 1.16 introduced some weird logic in the distinction between client- and server-side stuff and I can assume that this issue falls into that category somehow, but I'm not sure how to resolve this issue off the cuff.

@UnicornSnuggler [instance]/config/pamhc2crops.toml is a COMMON config. This means that the settings within are universal across all saves and are present on both client and server. On the other hand [instance]/saves/[save]/serverconfig/pamhc2crops.toml is a SERVER config and is generated new for every world unless, as you discovered, you put a version in defaultconfigs which will be used when a new save is created. In forge there also exists a CLIENT config. Each of these are separate configuration files that are handled separately.

If you find a mod that is overriding the version imported from defaultconfigs you should definitely bring that to their attention.

Looks like the immediate solution to this issue is to copy and paste the config files into the [instance]/defaultconfigs directory. With that said, though, other mods circumvent this step entirely by automatically porting over the relevant server files, so perhaps this is still something that should be addressed.