First of all, yes, the battery will be user replaceable.
Second, caring for LiPoly/LiIon batteries has become sometimes more of religion than engineering 
The facts that I know are:
- they do not like to be discharged low
- they do not like to be recharged too often
- the last about 10-20% of charge cause the most wear
Years of experience of Thinkpad users where the charge controller can be software controlled show that battery packs can be kept alive a lot longer when a) avoiding recharge cycles and b) not charging them to 100% every time they get charged. Of course this is no guarantee for cells not to fail but it seems to help a lot.
So giving an alarm beep when reaching 100% does not help. Once it is charged it is charged and nothing can be done anymore. Every charger logic must avoid to continue pumping energy into them anyway since Lithium based batteries could be severely damaged otherwise, up to burning / explosion. So after reaching 100% the charger will stop charging and the device gets powered from the charger, which should keep the battery at 100% - without continuing to charge it. It just remains full, no power is taken from it.
Long story short in the Librem5 we will implement a smart charger chip that can be controlled by software - to some extend. Of course cut-off currents and voltages for our battery may get hard coded to avoid them being changed and create dangerous situations, but the charging behavior will be user changeable, like when to stop starching, when to start charging again and some other parameters. If you do not need the full charge you can e.g. select to charge it to 90% only and not to recharge it before dropping below, say, 60%. This will save your battery quite some stress and it will last longer.
The details of this will be described in appropriate documentation we are creating while we make progress, some of you can already find on:
https://developer.puri.sm/
Cheers
nicole