Ok, i was thinking, maybe we are doing it wrong - maybe you are supposed to have own NavigationPolygon and what you paint on your tiles is like "DO NOT WALK THERE" polys (so your walkable location is XOR between big NavigationPoly and small polys from tiles...
Or throw away the big NavigationPoly entirely - and you are walking "outside" of the tile navi polys.
Either way, what you paint on tileset is "do not walk here". And if thats true, Godot team did a poor job telegraphing the idea.
Cant test it right now (dont have any free time :( )
Edit: well, i tested it and nope, doesnt work at all
Lets wait what guys say officially at your issue (worst case scenario is they tell us how to do it properly :) )
By the way, for capturing gif, i am using https://www.screentogif.com/