OK it seems I got the API enabled as well.
The entire process was this:
Install .Net 4 (which also installs .Net 2)
Let it restart
Install MBT Desktop 2.1
To run RegAsm.exe, it needs mscoree.dll. This was determined by attempting to run RegAsm.exe and it failed. Checking create log allowed me to see why it failed. So:
http://www.dll-files.com/dllindex/dll-files.shtml?mscoree
to get the DLL. Get the zip, and unzip it to the .Net 4 Framework folder. For me, in the path of the bottle itself, this was
/drive_c/windows/Microsoft.NET/Framework/v4.0.30319
Go to menu "Programs" then "Run Command…"
Select the bottle for this command to run under.
Use this command, taking care to change YOUR_BOTTLE_HERE to the path to your bottle
"YOUR_BOTTLE_HERE/drive_c/windows/Microsoft.NET/Framework/v4.0.30319/RegAsm.exe" "C:\Program Files\MBTrading\MBT Desktop Pro\RestAPI.dll"
Check "Create log"
Click Run. It may ask to save the log file "newlog" which for me was saved in the .Net 4 Framework folder.
It went through it's process and now says the API is enabled.