Why was the boat mounted this way on the underside of the wing on the "Landseaire" flying yacht?
The reason is the "flat tail" of the boat. The drag this "flat tail" produces when mounted "reverse" is much less then the dynamic drag it would induce the other way around.

https://en.wikipedia.org/wiki/Drag_(physics)




  I don't see how the link helps explain why the flat side produces less drag than the pointed side.– Ron Beyer 


The published cw coefficients (see answer of @jwzumwalt ) show the best value for the drop shape facing towards the air stream.

There is no entry for a reversed drop. But it is evident that is would have a higher cw coefficient.

A closer look at the boat reveals it also has a drop shape. But this is facing to its tail. Therefore the boat creates less drag when mounted "reverse".




  If this was the case, wouldn't the boat cause less drag moving backwards through the water also? – andy-m 


It might but the usually draft of the boat is no so deep that a relevant part of the "flat tail" is actually in the water.

source: https://upload.wikimedia.org/wikipedia/commons/2/2d/Bundesarchiv_B_145_Bild-F056332-0004%2C_Bonn%2C_Bundesgartenschau%2C_Seen.jpg

On the other hand a little turbulences at the boats tail could help to keep direction in the absence of  a steering paddel... 




  This explanation is wrong - an anemometer spins with the forward facing blunt half of the hemisphere causing the most drag - en.wikipedia.org/wiki/Anemometer – jwzumwalt 


The most important differences between the anemometer an the drag experiment is:
The half bowls in the anemometer are hollow which "catches" the wind way better than the flat surface of the filled half bowls in the experiment.