My working assumption after running into this problem is that the functionality Inventory->"Units of Measure" is incompatible with the functionality Webshop->"Product Reference Price". If UoM is switched on, the handling of product reference prices is messed up. 

So far, "Product Reference Price" behaves as expected after having turned off "Units of Measure". I have the luxury to do this for some of my clients, but not for others.

(Admittedly, this is so far a first impression, not the outcome after extended testing or productive use). 
 

Upon second thought, the real problem is probably: UoM is conceptually incompatible with Product Reference Prices. The two concepts have contradictory semantics for the "Sales Price": 

• For "unit of measure" (e.g. selling paint by the liter), the Sales Price *is the* price per unit. 
• But for "product reference price" (e.g. selling paint by the can), the Sales Price is the price for an entire package (a can, which is a multiple of the "price per unit"). 

(you could also consider that the two features imply different meanings for "unit" - the continuous unit like meters or liters in one case, and the discrete unit like canister or bottle in the other. The water-bottle-example unfortunately obscures this difference, that's why I used paint above.)

As is, there is no way for the system to determine which semantics to apply under given circumstances. Adding packagings only adds to the confusion. 

This possible in V16

1. Enable product reference price from website > configuration > settings

2. Provide the base units count on product page - price per unit is calculated basis the sale price

On website this is now visible

Also, possible to create 6 pack as a UoM in category units if you always sell as 6 units