As title says, if you change a toggle option in the Mod Integration config, it does not seem to be reflected in the checks in UTMixinLoader, so mixins are applied regardless of the checks, only depending on the default values. If the mixin classes itself have the checks, those still work as they are an extra safeguard.

As an example, let's add Blood Magic and consider utDuplicationFixesToggle. This is default true, but setting it to false in the config will still queue mixins.mods.bloodmagic.dupes.json even though the config option should be checked in UTMixinLoader. This means regardless of the duplication fixes toggle option, the dupe fix mixin will be applied. This can be checked through the debug log or by checking exported mixins after opening the Sigil of Holding in this specific case.

In other words, it seems that config values aren't read from file by the time UTMixinLoader checks the config. This doesn't seem to be a problem for the other types of mixins loaded by UTLoadingPlugin though. I don't know if this is an issue due to ILateMixinLoader or using ConfigAnytime.

Positively tested with the mentioned Blood Magic config!

Fixed with CleanroomMC/ConfigAnytime@0d59e37

Please try it with this build of ConfigAnytime: !configanytime-1.0-INTERNAL.zip.

(unzip before adding it to mods folder, since github doesn't allow .jar files, it is packed inside a .zip)