I've been on the quest to find this out these last days, but nobody seems to have any real answer and everyone is just going on about the houseboats.

However, I discovered, to my frustration, that pets (cats, dogs) can't sit in the boats when travelling between points (example mainland to an island)?? They can go in the taxiboats, but they cant sit in the sailboats and motorboats? How come? Or am I missing something? I kept trying to have my sim invite the dog on board, since it couldn't board. I tried moving the boat between mooring posts, thinking it was since the dog cant go in water (makes no sense since they just teleport anyway.)

I've tried only the sailboat and that motorboat you can waterski from. I did not try any other boat.
Why was this made this way? What was the point in not adding them to boats when everyone in boats are just sitting there anyway? I just....I am so confused.

No, not missing something, pets can't join your sim in a boat. You'll have to ask EA why, lol. I find there's quite a number of these little things that make me wonder, why didn't they, but maybe we are expecting too much.

This is core blocked so you won't accomplish it. It was an easy cop out because they don't require rigging, animations or logic of what happens if there's no driver if they are hidden in the taxi boat that drives it's self.