The article linked above refers to formats with 10-bit and 16-bit luma (when no color subsampling is used, they are also referred to as 30-bit and 48-bit deep color).
YUY2, with 8-bit luma, is 16-bit overall because of color subsampling. Your
Huffyuv that is being reported as 24-bit is very unlikely to actually be 4:4:4, so it isn't really 24-bit. I don't think
Huffyuv even supports 4:4:4.
Bottom line: both files are most likely using the same color format, and there is nothing to be concerned about. Compress your "MS-YUV 16 bit" captures with Huffyuv, open them in
VirtualDub, and check the Compression property. It will probably say 24-bit even though they aren't.