Miguel,
Typically, and I say typically, there should have been a bead of bonding putty tying in these bulkheads to the underside of the deck. These are bonding surfaces. Why wasn't that done? Someone most likely didn't feel like doing it that day your boat was decked, or schedule demands required them to do less then the proper job. Hate to say it, but that sort of thing is common in the boat building business. Trust me, I've been in the business for 15 years.
A piece of advice. If you can fit 2" PVC pipe, or even larger, without any fit interference, DO IT! The bigger the pipe, the better. It will just make your life easier further down the line when you may want to re-power, add some electronics, re-wire, whatever. Trust me on that one.
Any other questions, feel free. 8)