This might be fixed now, check out latest beta:
- The NuGet search engine now recognizes SemVer2 prerelease packages, and uses a new faster API.
- LINQPad now identifies NuGet packages with duplicate extension attributes in Content_Types.xml, and automatically removes the duplicates so that the package loader will not throw an InvalidOperationException.

I can see that it does not work from the LINQPad Nuget Manager (even with prerelease flag activated).
However, SemVer 2 is partly supported through explicit version naming by manually editing the .linq file.

Ex. Supported (explicit version):
<Query Kind="Statements">
<NuGetReference Version="1.2.3-a.1234">MyGetAssembly</NuGetReference>
</Query>

Ex. Unsupported (wildcards etc. not supported):
<Query Kind="Statements">
<NuGetReference Version="1.2.3-a.*">MyGetAssembly</NuGetReference>
</Query>

Since the '1.2.3-a.123' assembly does not show at all in Nuget Manager, but does download and load if set manually. I would consider this more of a bug, than a missing feature.

Right now it does not seem to work with format like: 1.2.3-a.1234, even though I have checked include pre-release.
Newer version of NuGet should help for SemVer 2.0.0.

Right now NuGet 4(.x) might be the target for this one instead of 3.