There seems to be a lot of confusion and in traditional Mozilla fashion all this is poorly communicated.
First, Flash no longer gets updated for NPAPI (Netscape API) which is the way it talks to Firefox. Only PPAPI (Pepper API) gets updates, which is what Chrome uses.
Mortar adds support PPAPI and deprecates/removes NPAPI.
It does not mean you need flash or that it adds stuff you "don't want". It just means it still works for the people who need it - that's it.
By that means it also means any other PPAPI plugin works, so the PDF reader too. It doesn't mean PDF.js (Firefox' own reader) goes away. It just means you can also use PPAPI stuff. If Chrome's PDF reader ends up being better than PDF.js over time, then they can switch over to it as default.
It's not using Chrome's rendering, layering, etc. engine. It's not using Chrome's UI. It's not browsing the web with Chrome, at all.