To reiterate, your modeline is irrelevant when using direct video, its just using whatever resolution the core decides on. So yes the direct video resolution settings are different, but you can't control them!
Direct_video seem to pass through some modifications of the analog signal that will not appear from HDMI otherwise. Ypbpr and csync in the ini normally only affect the analog out, that might be passed along HDMI when you use direct video. I'm not so sure about the SoG switch.
I don't know how your "VGA adapter" is connecting to your TV. I'm assuming its HDMI->VGA, and then VGA->?. You might need to find a more fully featured adapter if you ever want to move beyond direct video, or else get a working I/O board (which can use ypbpr/csync in conjunction with vga_scaler)
I will say direct video seems to display 200p DOS games pixel-perfect, just maybe not centered where you will like. 720x400 DOS OTOH will always be slightly ugly (though still readable), though maybe by changing the vmode within DOS you can get around that.