I just noticed that Zilav might have already answered my question when I asked him about plugins and navmesh overrides:
Yes, you can mod any plugin and any content with another plugin, and then another one on top of them, and another... up to the 253 plugins limit. That's the buty of Beth's plugins system.
Make sure to convert plugins being modded into ESM (toggle flag in TES4 header) when loading in CK, no need to change extension.
Toggling Jaggarsfeld to be an ESM while I work in the CK might be the answer I've been looking for as long as this change doesn't require the main mod to stay an ESM in the header...which would require a mod update to Jaggarsfeld...which probably wouldn't happen... I must try this when I get home from work tonight!
If you are working on a plugin inside the CK every master must have the ESM flag, if you fail to do so then the CK will not save it as a master and break any reference to the plugin. Just like deleting a master in the CK.