?
This was a breaking change NuGet team made in NuGet 3.4 (I think). We did not want to not implement, as the change would impact a lot of our customers who rely on the quirks of "non-normalized" versions.
So, as a compromise, the NuGet team implemented a searching strategy in the client to try a normalized version of the number (like 0.0.0.0), and then try non-normalized version (0.0.0) if not found.
At this time, you'll need to do the same for your searches; if we ever decide to implement the normalized version, this strategy will be backwards compatible.