So why two configs?
If I can't edit the vanilla file, what's the point of this plugin? I've been using this plugin for 3-4 years, and you seem to be a new dev that took over this project and completely overhauled it with less features?
You're dense huh? This'll be the last time I repeat myself.
1. There isn't and never has been 2 configurations. Configuration files are stored under oxide/config. You will see there is only 1 configuration file.
2. Under oxide/data is the DATAFILE not configuration, a datafile is not intended to be modified, and never has been since oxide was first created. Moving stack sizes to the configuration was correcting my mistake, and the mistake of other maintainers to provide a less confusing experience. Datafiles are like databases, the user should never ever touch them, that's why there are configuration files.
3. Again, you edit stack sizes in the configuration under the value IndividualItemStackSizes, which is populated when the plugin is first created. It functions EXACTLY like the datafile, it's just in the configuration where it should have always been.
4. I'm the original developer of this plugin, which initially released on the old Oxide site roughly 7 years ago, and has since gone through at least 1 different maintainer, I honestly didn't keep track of it. I initially stopped updating it because my life was crazy, so other maintainers kept the lights on, thankfully. Then I reaquired the plugin, which largely hadn't been changed much, granted it's a rather simple process to change stack sizes. If anyone is new here, it's you. I believe back then my username was Waizujin.
5. Pretty much the same features it's always had are still present, although I did regress quite a bit in v4, as the hooks I was using were causing more issues than they were solving, and causing quite a few plugin conflicts, so I brought it back to the basics, primarily to build a strong foundation, considering this is one of the main plugins used by servers for 7 years. I'd rather maintain a solid plugin, than a buggy featured plugin.
So once again, there isn't 2 configurations, and hasn't been since I created it 7 years ago. You're using it incorrectly which is why it's display unintended behaviour, user error. Modify the configuration values under InvidualItemStackSizes in oxide/config/StackSizeController.json and solve all your problems, or continue to repeat "why two configs" until you're blue in the face. Regardless I can not make this any clearer without literally doing it for you. I will not provider further support or continue this discussion. If you still haven't figured out how the plugin works, I strongly encourage you locate one of the other plugins providing similar functionality.
Jesus christ man.
EDIT: Last ditch effort to identify where the disconnect here is; I want to state the reason there is still a datafile, which isn't a configuration file as it's name clearly indicates, is because Rust doesn't store vanilla stack sizes, so when you unload the plugin stack sizes stay the same. The datafile is there solely to ensure when the plugin is unloaded, that vanilla stack sizes are configured correctly without a server restart. The plugin does rely on this file some, and in a way that REQUIRES the file to be unmodifiable to prevent bug reports due to user error.