I don't use the method you employ. But prefer kssh from the kde community repo.
You basically just connect via the terminal, once logged in to the remote box, just start apps: eg: firefox
For file management I connect via konqueror with: fish://
Multiple instances of the same application should be fine.
But I'm not sure about
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BTW, I am logging in to the remote machine as a different user than the one which might be logged in
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