The PhoneGap desktop app is not linked to build in any way. If you are adding the config file to an existing project you will need to use the option to "Open existing PhoneGap project...". To use build you will either need to use the web interface or the CLI.
It is my opinion that the PhoneGap team has given up on Windows 10, as they do not answer any forum questions on it, or provide any documentation updates. The other reason is that Windows 10 Phone Gap Builds (PGB)fail 20% of the time in the morning here in the UK, and 100% of the time in the afternoon in the UK. This smacks of a lack of interest in fixing very important bugs.
Finally, when we are lucky enough to get a .APPX from PGB, it crashes immediately after launch, whereas the exact same code is sent through PGB to generate perfectly operational iOS and Android apps.