If you read the README in the VGA install, vs the README.TXT in the install that does not say VGA, you will find the VGA is the lo-res VGA version.
And in fact, the non-VGA version is the Hi-Res version that runs at SVGA 640x480 instead of the lo-res 320x200 VGA floppy version (which is included on the CD version). So, it is not in fact EGA, unlike previous games with two version. This is the first SVGA Sierra game I believe as well. It can be very difficult to tell, but it is using much more than 16 colors in the beginning hotel scene alone, and certainly not usual EGA colors.

ScummVM Wiki confirms the HiRes version is 640x480 and 256 colors. And is supported as of ScummVM 2.0, which is often why you see the lo-res version most times, as it was supported earlier. I am not sure of the timings, but ScummVM 2.0 probably was released after GoG released the LSL series. So, hires LSL6 still uses DOSBox.

Also, when this was originally released, those who had 386SX or older could only use the VGA lo-res version. And, to be blunt, the lo-res was smaller overall and easier to.... illegally release pirated crack on BBS boards where download times over a modem was a thing to pay attention to. Which is why the VGA lo-res is probably more common and known to most.