Apparently this is not a bug but a feature!
The way the process works is rather simple (and this is why I missed this before):
When a user changes their penumbra mods, it will send the server a list of hashes. The server will then respond in kind with the necccesary uploads (we only upload the files we don't know yet on the server end). When the user uploads a first file, the fileserver sends a notification to all local pairs of the given user via signalr directly. This is why you see "Uploading....." only on the local end.
I've introduced a new cross-federation command that will add on to this way of processing.
Whenever a local notification is sent, it will now trigger a federation command sent over to the other servers (according to the way all of the x-federation call are done).
This results in a working scenario, where every client sees "Uploading...." at the same time, or well, nearly. the "downloading" message (with hthe file sizes and such) is a different call - and this already worked properly.
Merged in: https://git.honse.farm/astraea/honse-farm/-/merge_requests/49