AutoModpack should work with all minecraft modifications (it would be a bit bad modpack updater if it didn't). However, there are some exceptions and limitations that you should be aware of:

• Majrusz's Mods: Requires a modified Majrusz Library to work with AutoModpack. Github Issue. Or forceCopyFilesToStandardLocation in server config.
• CITResewnNeoPatcher: Requires to specify fabric version of CITResewn in forceCopyFilesToStandardLocation in server config, like (/mods/citresewn-1.2.1+1.21.jar).
• ModSets: It's currently broken due to similarities in mod loading modification process.
• Cesium: Cesium is currently incompatible due to wrong way of zstd packaging on AutoModpack side. It will be fixed soon. GitHub Issue