The Windows version, like the Linux version, is a port of the original OS X version. It uses a bitmapped version of the Monaco font as rendered by OS X; this font, in each of 13 sizes, is stored in the fonts subfolder. To change the font size while playing Brogue on Windows, press -/+ or pgdn/pgup.
The Windows version of Brogue supports all the same switches as the Linux version, except for terminal mode. To use a switch on Windows without resorting to the command line, create a shortcut to the Brogue executable, right click and view its properties, and then edit the shortcut's Target. If there are quotes around the name, put the switches after the closing quote, like so:
"C:\Users\Rodney\Desktop\brogue v1.6.2\brogue.exe" -M --size 9