To the OP's question, I would find a page number in the middle of the page quite distracting. I don't like it, it looks clunky.
As to the problem of pages, I don't have one. Each book I buy I download and load into Calibre. I have set up a custom column #pages# so I write down the number of pages in it from the edition I want from Goodreads.
For example I downloaded Barsoom omnibus from MR, then I've split it with epubsplit and for the first book "A Princes of Mars" I've typed in this edition number
https://www.goodreads.com/book/show/...incess_of_Mars
So now my book shows 160 pages on paperwhite. It might be straightforward and simple but it works for me. I just type in the page number I want. I don't use Estimate page count or Download page count, because I don't see the reason to do so.
When I read an ebook I always update my goodreads with page number. It might not perfectly correspond to paperpack but it works for me, 1 page or 2 difference, don't matter to me. I dislike percentage updates/way of tracking, but I find time left in chapter useful.