Nah, get out the drill and a fekin great rasp, it'll be fine.
Don't just put a piece of tube through there held in by sealant, you'd be asking for trouble.
If you want it to work well, you need the biggest radius possible on the inside.
The best place for the drain is in the corner of a transom well.
1. Get a clean and empty plastic grease tub.
2. Make a hole in the transom about 10mm larger in diameter than the tub.
3. Radius the inside of the hole as much as possible.
4. Rough up the area around the hole a fair way back on the inside. Use the rasp, course abrasive paper or whatever you have.
5. Lightly chamfer the edge of the hole on the outside.
5a. (I forgot this bit.) Mask up the outside of the transom and neatly cut around the edge of the hole.
6. Laminate right through so as to join the inside and outside of the transom. Make sure it is really sound.
7. Wet out strips of csm and wrap them around the plastic tub until it's about 3mm thick.
8. Force the tub into the hole until it protrudes at the back of the transom as least 25mm. Stipple it to neaten it and allow it to set firmly.
9. Take a block of wood and a hammer and give the base of the tub a whack. It will pop out because it is tapered and, also, the resin will not adhere to it.
10. Trim it all and remove any ragged bits.
11. Give it a flow coat to match the rest of the boat.
12. Measure around the new flange and add 20mm for an overlap.
13. Measure up the transom, from the bottom edge of the hole, the distance you want the trunk to reach and add on about 40mm.
14. Cut a length of hypalon to these dimensions.
15. Glue the hypalon into position on the flange and as the corners come together also bring together the join along its length to form the tube.
You can tighten a Jubilee clip around the flange to apply firm pressure to the adhesive to ensure a good watertight joint.
I presume you know how to glue hypalon.