Doesn't this cause a problem where two buildings on separate transformers are serviced by a common metallic waterline?

With the common grounded conductor on the medium voltage side, on the above drawing, the neutrals are connected at the transformers and the neutrals at the buildings are connected through the common waterline where they are bonded. I assume you bond your waterlines.

This would put the neutrals from the two transformers in parallel. If a neutral to a large service on the large transformer failed, the entire neutral current would run through the neutral for the smaller service fed from the smaller transformer. The neutral and ground system might be too small for the load.

Here, with a resistance of even 10 ohms between ground systems (and neutrals) the current on the wrong system neutral would be limited to about 12 amps.