I have Windows FTP running and it still installs in Program files or C:\. It used to install in ftproot.
Of course if you are familiar with managing FTP you can use multiple directories with different loads and just change the ftp folder to the one you are working on.
As to the built in FTP!
I was happy to see that option and did my last upgrade that way.
Guess what? Things are not the way I thought they are.
I assumed that the installation files are going to be transferred to the system first, then run from there without my computer. Wrong!
The FTP on the system uses the directory on my machine. It makes it slower to load. I was upgrading a three member cluster at the same time, running three FTP servers on the three systems, and they waited for each other to pull the files.