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: Require a modified Majrusz Library to work with AutoModpack. Github Issue.
• 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