So it turns out that the Mediator 4000di Mk. I is *actually* incompatible with the A3640 - it just can't execute anything from ZorroIII-mapped memory addresses.
I have finally tested my system with a CyberstormPPC (which was lent to me thanks to EAB user @reflex) and I could execute stuff from the Mediator memory without any issue. Which also solves my troubles with the Sonnet library and the Killer M1.
I will also send a message to @gsoravil as he has been having the same issues with his Mk. I for almost as long as me
I hope that this info will be useful to other users.