First option (
https://akkuplus.de/Einzelzelle-5050...mAh-Li-Polymer) is absolutely type that you want, also it is 5 mm and more appropriate for installation in device). PCB stuff is basic electronics which controls some battery functions and is good to have as some basic level of protection and battery charging/discharging control.
Capacity of 2000 mAh is adequate for everyday usage of Inkpad 3. Original battery (which was 1900 mAh) provided around 7000 page turns, so you should be satisfied with that
Long time ago, I experimented with my old trusty Kindle Touch (8th generation). I installed mega battery (around 3000 mAh) which lasted forever
But I removed back cover and made custom homemade cover which was cumbersome... It was not that great experience...
Convinience which you have with slick and thin device is more important, trust me