eBooks from Amazon Market or from Android Market? I have finally succeeded at Rooting and installing Android Market on my Fire, but now I'm wondering if there are any complications with using both the Market and Amazon to purchase ebooks.

Scenario

Say that I want to purchase an eBook and that book is available in the Android Market and the Kindle Market for the same price. I need to build some foundation in order to make a decision, here are my concerns:

Concerns


Does an eBook from Android market have a different format than a Kindle format eBook?
If so, Which one should I buy looking forward? Android Market seems to be more open while Amazon even though they are using Android they follow closed practices similar to Apple. However, Amazon is a big book seller and a strong innovative technology company.
I also have a lot of books in PDF format. Which app do you guys recommend for reading PDF from Kindle or any other Android device?
Which is the best app for reading mobi format eBooks?
Yes, an eBook from Android Market (in Google Books) has a different format from the Kindle. It would seem that you can obtain Google books in either ePub or PDF (more information here). Amazon books are in the AZW format.
This comes down to personal preference. I have read books on both Google Books and Kindle on my Xoom; I see little to no difference in quality. Both can sync to my phone to keep my place. Since you have a Kindle Fire, perhaps sticking in the Amazon ecosystem would be a good idea, since you may wish to un-root in the future.
There are a lot of PDF readers; just recently the Kindle software was updated to read PDFs. I personally use ezPDF Pro for PDF files because of speed and its ability to remember my location in PDF files from read to read.
This again, would be personal preference; however I have loaded Mobi into the Kindle app without problems.  The book acted like any other I had in regards to reading (except it did not sync across devices and had to be manually uploaded to each of them). I would suggest looking at this question as well for more information on eReaders.


So, the Kindle App does what you want it to do overall (Books, PDFs, and Mobi) and also is a major part of the Kindle Fire Amazon Ecosystem they have setup for the device; and may be the way to go if you decide to revert your Fire to its un-rooted state.

Edit (Addition):
Amazon also seems to like releasing updates that Un-root your device (and prevent further known rooting methods - for now). Source states that unless you have changed ROMs, you are susceptible at any time on WiFi to get the update.