When I open the signal GUI there are 2 signals with the same sprite, same name and very similar description for the Boat, but one has "Consumes burnable fuel" while the other has "Vehicle" in their description.

What signal GUI and other mods are you using? There are actually three "boat" entities. One is of type "car" (drivable vehicle), one is of type "cargo-wagon" (waterway train), and one is type "locomotive" (invisible and automatically attached to the boat cargo-wagon.

It could be that your issue would be resolved by giving boat and boat_indep unique localized names.

Here is a link to the save file: https://www.file.io/nBGv/download/ENhLnkcSgU3z (the file will expire on Apr 3, 2023 1:57 AM)
And here is a link to my settings.ini file if needed: https://controlc.com/fcd4b14d

I am using the GUI for setting up logistic filter in the yellow logic chest. It's also visible when selecting an icon for a train stop's name and other places where icons can be selected.

screenshot: https://imgur.com/a/8KOD4Db

Okay, yeah. There is a dummy item for the boat-wagon because at least at one time, there were some limitations on entities without associated items. It's probably not clear which one refers to the actual craftable item, so I'll take a look at it.

Not sure if this is what you were seeing, but Gizmo's Car Keys adds a third boat item in the logistic request panel. We'll look at them both, thanks.

There is the DMV mod which makes spider-vehicle versions of all car-prototypes and hides the original recipes. Unfortunately, it will also change the place_result of the original item, so that it will point to the new spider-vehicle fake car. GCKI will derive the vehicle icons shown on its GUIs from the place_result of an item, but can't find it when DMV is used. Therefore, I create a dummy item if DMV is active.

I've already fixed that for the next release of GCKI, but there's still another issue I must resolve before I can upload. Meanwhile, you can unpack GCKI and add

new_item.flags = {"hidden"}

between these lines (33-34) in prototypes/3-recreate-car-items.lua:

  new_item.place_result = car.name
  data:extend({new_item})