Assuming you're running on OSX/Linux, you can make a quick bash script that just ignores any additional arguments, and use that script as your "cmd"
. Save the following in ~/bin
as makeglossaries_main.sh
:
#!/bin/bash
/path/to/makeglossaries main
then change the relevant line in your build system to:
"cmd": ["/home/adrian/bin/makeglossaries_main.sh"]
and you should be all set.