I wish to add only a few pages of my website in different folders. The only way of doing that I can think of till now is by creating a completely different Muse file and uploading it all in the required folders which alos forces me to make an index.html page. Also, I can manually change move the HTML files to the required folders but that will need me to edit the URLs in those as Muse doesn't create absolute URLs or I'll have to keep on duplicating all the folders - thus wasting my server space. Is there some other way in which I can upload only a few pages of my website in a different folder on the server?
No this isn’t possible. Why do you want this?
As you said: The only way to achieve this, is using a different domain/subdomain.
I kind of needed it for a particular type of integration with my Android app, but seems, another Muse file is the only way to go.