It’s always hard for me to spot boards like this where you can actually keep your NV mat under control for most of the game.
I didn't predict perfectly how it would work before game 1, but I got the basics right: Navigator lets you peek and steer, which makes it possible to set aside only junk with NV, and it's possible to play Navigator first followed by NV thanks to +1 action from either Tactician (most of the game) or Bazaar (early and only if you're very lucky).
The heuristic I used in deciding to go for it was "it is possible to know the top card of your deck somehow, and then play Native Village". That's probably a good first guess, but with room for refinement—connecting Native Village and Province has a high probability of working because the deck is relatively thin compared to the number of Navigators. If I had one Navigator in a 30-card deck it probably wouldn't work.
I would have traded two Navigators for two Merchant Ships, but I suppose it’s not that important.
I did some test plays of this. The two decks take somewhat different routes to the same destination, and it feels very potayto-potarto to me which one you take.
Let's state the obvious: due to the duration effect, Merchant Ship is one less card to draw and one less terminal to play.
With Navigators you're under-terminaled by 1, but you can't really cut any villages because they provide money and thinning. The effect of being under-terminaled by 2 is that you're a little more likely to have more villages than terminals in hand than otherwise, but if you start your turn with Navigator you're likely to be fine in any case.
The deck draws 16 cards: clean-up 5, Tactician 5, Bazaar 4, Ghost Ship 2, independent of Navigator vs. Merchant Ship. It wants to draw 13 or 14: Tactician 1, Native Village 2, Bazaar 4, Ghost Ship 1, junk 1, Navigator 2 or 4, Merchant Ship 2 or 1. It also wants to set aside 2 with Native Village, although it's okay to miss once or twice.
This suggests that if you get Ghost Ship played on you, the more Merchant Ship heavy build is more resilient; it can have 4 Provinces (1 junk discard, two set aside, overdraw by 1) and still draw itself just fine, where the Navigator build might stall.
I think this suggests that Pearl Diver is more helpful in the Navigator-heavy build: if it has 4 provinces in deck, it can use Navigator (with 6 cards in deck) and Pearl Diver to select which card to underdraw. The surplus of Navigators can help you push junks towards the bottom. Also, switching from using Pearl Diver (or any cantrip) to Province as Tactician junk effectively lets you absorb one junk card for free.
But if you ever have 4 Provinces on deck, it's because you missed matting some for several turns in a row, so most likely you have 4 in deck and a couple on the mat, in which case you have already won ;-)
So... potayto-potarto.
In favor of more Navigators: only having 2 makes it a little more likely that you won't have any in your starting hand; also, against Ghost Ship you have to get through an 8-card deck with the aid of "only" 2 Navigators. Most of the time you want to not discard to the first (because you'd be either drawing or matting an unknown card with Bazaar or Native Village), but if the second navigator is in the bottom 3 cards you might have to draw some blindly. It's not the worst thing in the world, but it might cause you to miss matting a Province more often than if you have more Navigators. On the flip side, your thinner deck can afford more of this.
So... potarto-potayto.
I'm sure someone could run simulations or do some heavy-duty math and calculate that one build has a 0.1% higher risk of dudding, but... man, I have better things to do with my time
Also, I hadn't even considered what to do on dud turns. I guess Province plus some combination of one extra Native Village and an alternation between Ghost Ship and Bazaar. That is, increase your thinning rate to get back in control of your deck, and add more draw and enough villages to support the extra draw. But the deck never duds, so this is purely academic