Yes, .NET 4.0 assemblies will work in a .NET 4.5 project. The 4.5 CLR is a new version of the CLR but is backwards compatible with 4.0. See this StackOverflow question and this blog post from Scott Hanselman.
So if you have a class project which is set to target .NET 4.5 and add the .NET 4.0 version of FluentMigrator as a reference (or install the Nuget package) then it will just work.
For FluentMigrator there is no major benefit of having a .NET 4.5 package, due to having to support .NET 3.5, none of the new .NET 4.5 features can be used yet.