WiX v3.5 is currently in beta, which will be released soon. This latest addition, Burn, is a bootloader / chain designed to do what you need.
WiX is a steep learning curve, mainly because you need to learn how to use MSI to do something slightly complicated. But it meets your requirements.
My choice is likely to be NSIS just because installer scripting is so simple. Although adding a .NET premise is manual, how to do it is well understood and published freely.
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