I finally had the time to make some changes to the project. The major difference is the switch to a STM32L071KZU6 MCU, comming in a different package. Other differences are the add of a decoupling capacitor and the 180° rotation of the battery connector. I removed the old files from hackaday, and will put the new ones once I have more time again. The files are available from the CircuitMaker project page.
I already ordered the PCBs, but this time with a ENIG finish and 0.8mm thickness. I'm expecting to get them around mi-January.