As Pawel said, IronPython uses a complex build system to handle all of the platforms it supports and make it easy-ish to add new ones (at least until IronPython and the DLR can be refactored into portable libraries ... sometime around 2016). In this case you need to dig through a couple of levels of imports to find where it's defined (Build/Common.proj
).
The reason this happen is that even though the Reference is conditional (and handled correctly) in MSBuild, VS ignores the conditional check and displays any Reference elements it finds. Moving the Reference into Build/net35.props
instead should fix the display, since VS does a much better job of handling imports.