My question is about Interface limiting / queue.

Suppose I have a eoip_interface that runs over the ether1 because ether1 is my internet conexion. If I set any policy over ether1, is eoip_interface also affected? Let´s say changes in MTU, rate limiting, marking packets that pass through the ether1... aslo affects to the eoip_interface?
I hope this question is clear.

Thank you very much

No, except MTU, i am not sure about that...

it depends )) if you mark all packets in 'output' chain and with out-interface=ether, then you will mark all encapsulated eoip packets