Are Thunderbolt/USB Type C in Late-2016 Macbook Pros compatible with non-Apple devices?
USB Type-C is a specification for a plug connector. Thunderbolt is a specification for a transfer protocol.

The original Thunderbolt, in mockups prior to its final specification, showed a USB Type-A connector being used. The USB Implementers Forum refused to allow the USB Type-A specification to be used as a combination port, so the Mini DisplayPort connector was used instead. Thunderbolt 2 used the same connector.

The link from the Wikipedia article you linked, to "Thunderbolt Alternate Mode" (being an alternate from a USB transfer specification), explains that Thunderbolt 3 uses USB Type-C connectors.

The port is not masquerading as anything: Because both Thunderbolt 3 and USB Type-C devices use the USB Type-C connector, all devices that have USB Type-C connectors and that have macOS drivers, or that can operate using drivers built into macOS, are compatible with the port, as are all Thunderbolt 3 devices (ditto regarding the drivers). Thunderbolt 1/2 devices are compatible through use of an adapter, as are USB devices that have a Type-A, Type-B, Micro-A, Micro-B, or Mini-B connector.