I have problem to determine, if the arduino shield connector is really arduino uno r3 compatible.
In doc FM4_AN709-000010-1v1-E in the section 3.1.2 it is ¨written interconnects provided for the standard Uno3 Arduino Shields." - I understand it that way that it should be compatible with Arduino Uno R3 shields. Thinking this way it should be 5V tolerant.
On the other hand in the doc 002-04980 Rev.*B as 5V tolerant inputs are mentioned only 'N-type' inputs and in the chip s6e2cc LQP-176 as in the SK-FM4-176L-S6E2CC devboard only pins 14,15,18,19 are described as 'N-type' and they are not even connected to arduino shield's connector.
How is it really with the arduino uno r3 shield compatibility?
Your explanation is correct. The SK-FM4-176L-S6E2CC is a 3V3 system. But Arduino/IOREF is connected to 5V, what may not have been a good decision. Please take care of the electrical compatibility when connecting external hardware/shields.