Boned Human Model importing to Unity 5.5 with incorrect bone rotations

I'm working on a project, where I've got a human model. This model will be used by players and certain NPCs. It has bones set up so that I can animate them in Unity using the Mecanim toolset, as well as manipulate them in certain ways using C# scripts.

There's one problem - while most of the model imports correctly, the two root bones - UpperTorso and LowerTorso - import to Unity 5.5 with rotations that are not 0, 0, 0. Specifically, UpperTorso imports with 0, 0, -90, and LowerTorso imports with 0, 0, 90, as shown below.



Because the model in question plays an integral role, and there are scripts that require rotation along the X axis to work properly, I need to figure out why this is happening, and ways that I can fix it. While I could write a hack to figure out how to properly rotate from the messed up state, I do not want to do that unless I absolutely have to; I'd like to learn to fix the model to meet my requirements.

The model is shown below, with bones and the containing 'empty', and the entire hierarchy for the file shown:



Question - In what way can I fix my file to fulfill my technical requirements, or is this a bug that needs to be reported to someone?

Edits - Grammar, missing words, general clarity.