For your first question, I will say that please make it clear.
This is not the way VTP Pruning works.
For the second question, Ether-channel to work between two different switches the speed and duplex should match.
Not only this there are some more important things to match for layer2 or layer3 ports.
If anything would be miss-match then the port will show legend S means Suspended mode.
1. If you are manually pruning, the frames will not be allowed to go through the trunk.
2. For EtherChannel to work correctly the speed and duplex should match for all the physical ports on both ends. Have you tried on real equipment, that can really help in solving this question. EtherChannel can be a pain on a real device too. If you can, please try the same using real devices.
3. It is possible to have an EtherChannel without trunking. You mentioned native vlans and allowed vlans. Are you configuring a trunk between the switches too?
All the best,