Though canoe does not have a deck, you may want to coat it as if it was the case.
First, the top/inside of the gunwales cannot be covered (easily) on the same day when you do the bottom. This means you need to wait till the bottom cures and coat them then.

Second, as you mentioned, the bottom of the canoe is important. The Goop may or may not penetrate well, depending on the fabric you use, your technique, temperature etc.
Hence, you may want to consider coating the inside of the canoe as well.
The additional benefit would be extra waterproofing of the inside, so if it gets swamped, the fabric will stay dry.
If you coat in 2 steps, you simply use paint masking tape to prevent drips.

As for dye, the same story as with goop. It may or may not penetrate all the way. However, once you do the exterior, you will see how well the dye penetrated to the interior, and touch up the interior only if necessary.