Source? Sure, it's theoretically possible that a TB3 5K@60Hz monitor won't work when plugged into a USB Type C port. But there would be no good reason for that, it should downgrade smoothly to either 5K@30Hz or 4K@60Hz.
I'm running off of the assumption that Thunderbolt continues to use a different physical layer (which it pretty much has to to go faster than USB 3.1), and is piggy backing on USB Type-C's "Alternate Mode" which lets you negotiate different physical layers that you have a transceiver for.
Sure, but why wouldn't the TB3 transceivers be designed to support USB 3.1 as well? Those transceivers have a wide range of dynamic adaptation to support high speed transmission, so it doesn't seem like much of a stretch to adapt to USB 3.1 signalling levels & protocol.
Because even above the physical layer, the two protocols are very, very different to the point that you're nearly doubling the amount of work that you have to do. USB at it's core is a host polled interface that looks like a network, and Thunderbolt is at it's core a multimaster RDMA interface. You'd basically be designing two different devices.
EDIT: Looks like my assumption is correct:
http://en.wikipedia.org/wiki/USB_Type-C