So, after many experiments I'm sorry to report that the RS-485 Atom module has very bad Rx characteristics.
The issue of getting corrupted data was related to problems in the serial support of the arduino-esp32 project. After moving to git version I still had several problems:
- missing bytes
- zero byte at end of rx block
- last byte of block was sometimes corrupted
I've then tried replacing the RS-485 Hat with another RS485-to-RS422 adapter and since then it works flawlessly. Something in the electrical design of the RS-485 hat must be messing up the Rx data.