???
The 'big' part of Calibre is usually the Library (folder), not the app.
That 'big' turns into 'Huge' if your Library is Manga
Using a hard wire connection to copy between drives is the fastest, with flas drives being a very slow Write (Rotating or SSD being on the fast end)
Are you compiling your own, because 'server' choices are part of the installed bundle, so I see little 'storage' saving when just using calibre-server.exe from the installed package.