Hey Joe, you are correct that if MAME sets the VGA resolution to 640x480 (or 1024x768), then the mini SLG will add scanlines to the image. If you have a MAME front-end and don't want scanlines for those screens, just run the front-end at a higher resolution than 1024x768.
I have not tested a mini SLG with a HDMI video card w/ VGA adapter, but as long as the adapter puts out a standard VGA signal, then scanlines should be added to the image (provided the resolution is compatible as mentioned above). However, depending on the quality of the adapter, it is possible there may be some interference in the signal that would impact the mini SLGs performance. For best results I always recommend hooking the mini SLG directly to the video source, running at 640x480 resolution.