Case I want to use is quite low, stock Odroid cooler won't fit (without modifications).

I found a 38x80mm radiator (from a dead motherboard), half of it was covered with a 1mm thick copper shim:

Cooler after cutting the shim in half, all parts are held together with a thermal glue:

Initial fit:

Original mount points are used:

And finished cooler attached:

SoC is the only part of Odroid touching the cooler, just like in original design.

Thermal surface shuold be big enough to be used without a fan (Odroid-U3 has a smaller one) but since there will be almost no airflow in the case there will be one.