I’ve been around the block with this issue on Discord a couple times, and ultimately I don’t have a solution. It’s certainly not something with Configurate (it’s not in the spec, nor can I replicate it), and it’s not TeslaCrate (it’s replacing values in nodes that aren’t accessed and saving a file that isn’t saved by TeslaCrate). Trying to escape them is a good idea and might do the trick.
My working theory is that this is being caused (or at least related) to the host’s file system. I’m not exactly sure what (or why) there would be anything here that could cause this, but at the end of the day options are rather limited. I think there might be some merit to the file encoding (as it appeared that there were differences in whitespace characters present), however this should not affect the default configuration as they’ll all made in the same way.
At this point, the best I can suggest is to test things wherever you can. See if angle brackets in comments are removed, and whether this affects multiple files (both within and outside of TeslaCrate), a single file (try renaming), or a file with a specific name (or loading order). If you can, try a different server and see if you have the same issue, and whether this only occurs for servers on that host. There’s not much I can really do about it, and I can definitively say that TeslaCrate isn’t the cause of this.