Hi Marek,
I reverted the changes step by step starting with patch 0002-remove-netdev_calls.patch, as patch 1 did not help and patch 3 containes in compat.h and soft-interface.c, I tried out myself earlier today.
The essential call is in patch 2 as assumed. As soon as I add the netdev_master_upper_dev_link call again to the compilable code, the problem starts to occur (mesh doesn't work as soon as bat0 is added to the bridge, ogm packets can be seen at bat0). It seems that this call behaves in older kernels different compared to newer ones.
I haven't tried to add all the other excluded parts again except for the netdev_master_upper_dev_link call. If you are interested I can test this tomorrow, too.
Regards, Andreas