Apple made a similar switch from one proprietary charging connector (magsafe 1) to another proprietary connector (magsafe 2) and it's a compatibility hassle between computers. For Surfaces it's an even bigger mess, because like you said, MS doesn't make them anymore. A coworker of mine had the same situation with a Surface Pro 1. Computer still works fine, but the power cord died, and good luck getting a replacement quickly. If you do find a 3rd party version, good luck with not burning your house down.
Real question to people in the know - is this truly the case?
I get that the port is industry standard, but are there electrical protections put in place?
If I use a 100W non-Apple charger on a MacBook Pro that uses a 63W charger will it damage the battery? Will a USB-C phone charger (with presumably very low wattage) work as well (albeit slower)?
While I really like that TB/USB3 ports are standard, it is incredibly confusing to laypeople with respect to understanding all the nuances.
This is the maximum wattage allowed under the USB Power Delivery spec [2], so any USB-C power supply should work. Maximum voltage/current is negotiated between the supply, cable, and computer, which should select the highest amount supported by all parts of the system.
If you're using a cheap 3rd-party charger that doesn't follow the spec and decides it's going to tell the computer "I support 100W, let's do that!" and then jacks up the voltage beyond the USB power delivery limits, then yeah, expect to have problems.
The problem that I actually imagine happening is people getting a 20W rated cable with their cell phone, trying to power their computer through it, and wondering why the battery continues to drain.
It'd be hard for me to buy anything that uses a proprietary charger ever again. This includes iPhones and Surface Books. And I've already committed to not buying anything that uses older versions of USB either -- it's all C for me.
My SP2 charger cable frayed near the power brick and I ended up just ripping the whole thing apart, cutting the cable & resoldering it. The enclosure was replaced with an off-the-shelf one. Looks ugly, but I didn't want to pay 100NZD for a third-party replacement.