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Pretty sure you should have the ability to choose what to sync, either from the server, or the client. Seems kind of dumb for it to automatically assume you have the space on the client device to sync EVERYTHING.
I thought the same thing, but I've spent a good chunk of time looking at every button in the linux client, and it's just options of "sync: y/n", with an initial choice of "do not sync if folder size is 500MB+". And the files/folders not synced do not show up locally. The windows client lets you see everything, but only download when you open or pick "save locally". But not on Linux.
Docs say you can choose what to sync, and disable syncing entirely where you don't want it: https://docs.nextcloud.com/server/latest/user_manual/en/desktop/usage.html
There should be a nearly identical menu to the Windows version that lets you select or deselect folders.
Click on your account > settings. And then it will show the list of folders available to sync.