i already saw those warnings a few times also, but i never noticed any difference.
Can you provide any examples?
i always thought that probably they're just being cautions...
There is one thing they don't have enabled by default (at least it wasn't the last time i checked), however, that may also bring that warning up: PDF Forms.
You can enable them in about:config searching for pdfjs.renderInteractiveForms and setting it to true (but they probably have a reason not to).
This will enable you to fill pdf forms directly in the browser.
PDF.js is actually a very good tool. It's actually (again, the last time i checked) more powerful than Chromes's PDFium