Some RIB manufacturers, eg Osprey, use a length of pipe (68mm downpipe, or 82mm soil pipe) through the transom, seal it in place and stick the trunk to the bit that protrudes out of the back of the transom. Others, eg Ribcraft & Avon, line the hole with GRP and use a trunk with a flange which is screwed to the outside of the transom.
Whichever way you decide to do it, cut the hole out with a good sharp core cutter. If you decide to use some pipe to line the hole, then drill the hole horizontal, rather than perpendicular to the transom face, to keep the trunks horizontal when deployed. Stick the pipe in place with plenty of Sikaflex, to prevent any water ingress.
If, on the other hand, you decide to use a trunk with a flange, then the angle of the hole cut out is less important. In this instance, I would cut some 2" wide strips of chopped strand mat and lay up 2 layers inside the hole against the plywood core, then finish it off with some flowcoat.
If you think all this may be beyond your capabilities, it may be worth having a word with Ribcraft in Yeovil, to see if they will do it for you.