Matlab is a VERY weak binary signature:
True, but there's also a string, and that lower the possibility (still present) of some false positives.
The "MATLAB program" definition is also very broad: probably it would be possible to keep that as a general one, and make some more specific ones, each for various versions maybe (I'm speculating here; I'm not really that familiar with MATLAB files).
It only takes takes a percent sign at the beginning of a file to be considered Matlab. All valid PDF's start with a percent sign, so they will show as both.
Yes but, if it's a PDF, it will have an higher score since the file will match a larger pattern specific for the PDF ("%PDF").