I think it is worth taking this one back to first principles (PHB p.6):
How to Play
The DM describes the environment.
The players describe what they want to do.
The DM narrates the results of the adventurers’ actions.
The environment consists of a desert and a boat-like vehicle. The players want to hide its tracks.
The PHB (p. 183) has this to say about tracking:
Track. A character can follow the tracks of another creature, making a Wisdom (Survival) check when the DM calls for it. (The Dungeon Master’s Guide has rules
And the referred to DMG info is on p. 254:
Adventurers sometimes choose their path by following the tracks of other creatures - or other creatures might track the adventurers! To track, one or more creatures must succeed on a Wisdom (Survival) check.
Now, if you want to take an absurd RAW position, no one can track the boat-like vehicle because it is not a creature and only creatures can be tracked. QED.
Assuming that you are going to be more sensible than this, you have to accept that "creatures" has to include their mechanical or magical mode of transportation. If that is how you want to interpret it then there is no reason that Pass without Trace won't do exactly what it says it will do:
For the duration, each creature you choose within 30 feet of you (including you) has a +10 bonus to Dexterity (Stealth) checks and can’t be tracked except by magical means. A creature that receives this bonus leaves behind no tracks or other traces of its passage.
Providing that each creature on the boat-like vehicle is within the area of effect (30 foot of you) then I see no reason why it wouldn't work exactly as advertised. After all, it expends at least a 2nd level spell slot per hour and is a Concentration spell so its not without cost to the caster.
From a pure realism point of view there is nothing to stop characters from mechanically erasing the tracks of the vehicle providing they are willing to spend the time, effort and have the necessary skill (Dexterity (Stealth) or Wisdom (Survival): use your best judgement). All the spell does is cause this to happen through magic.