I always observe 4.0xxV from the li-po battery attached after when thingy52 stopped charging.
I think this problem maybe because of output current from the battery charger (XC6804) is consumed by battery charging and system load at the same time.
AFAIK, XC6804 doesn't have power path feature so, it will be problem if there is no circuit to isolate current consumption for battery charging and system load. (I can't find related circuit to isolate and switch power source between VBUS and VLi-Ion in the schematic.)
Please take a look this issue and post possible solution for this.