A trunk is not really meant to be used between two different switches. You would be better off just using two separate network connections and letting the QNAP decide which connection is fastest/optimal. Trunking is really meant to allow you to combine multiple ports to increase the speed of the connection - so two 1 Gbit ports to give you a 2 Gbit connection, two 2.5 Gbit ports gives you 5 Gb, etc. Yes, you can set things up to give you fallover capability, etc. but that’s not really designed to be done across two switches. I’ve not really seen that.
So to attempt to answer your questions - I don’t think you can change the MAC address of the trunk. Why do you want to do that?
For question 2, I don’t think you get a choice over which is primary and which is secondary. That’s all handled by the protocol.
For question 3, I have never seen any ability to do trunks of trunks. Doesn’t make sense. A trunk is already an encapsulated tunnel where the traffic is split between both connections.What would be the purpose of creating a “trunk of a trunk”? The trunk already has redundancy built into it. I’ll have to try adding a trunk port to another trunk on one of my Ciscos…