Would it be possible to install a copy of UGENE on a remote Windows virtual machine simply by copying a folder rather than running a proper installation process?
Thanks!

Yes, just prepare the Virtual Box image with UGENE installed and add it to a Windows "Startup" chain.

Normally the installation for UGENE is not required, you can move it to any PC with just copying its folder. Note that UGENE keeps the paths to the plugins in UGENE.ini file, so if you run it once, move to a new location on the same PC and run it again it will keep using the plugins from the first location.
Remove UGENE.ini to make it look for plugins again, the current folder will be searched first.

Now we are working on a special server-only version of UGENE with improved stability, security, simplified installation. Check for a new release for more details during the next 2 weeks.