@François-Wautier This is a strange case. I have trouble believing the sysupgrade to b159 is causing your Omega to overheat ... Too hot to touch is too hot. Could the Power dock's power be out of Omega specs? If you have a VOM can you measure the voltage on that dock's VIN pin to GND? It should be 3.3 volts.
In my experience when the Omega2+ is run at a higher voltage (DON'T do this!) then the RF shield does become HOT to the touch. Also, this may permanently alter the unit's ability to work within normal specs, ie my unit that was powered at 4.7V for an hour needs 3.4V+ to boot and has developed other quirks.
Otherwise, the "too hot to touch" condition suggests a solder bridge on the board somewhere, causing a short between several of the traces. Do you have a means to measure that Omega's mA load while on the Expansion dock, ie with a bench power supply? A sustained higher than expected current draw ( .20 amp) is the sign that you have a short.