Sigh...I'm so sorry, Eli. I am completely befuddled by this problem. I have absolutely no idea what's going on.
Thank you for testing with more than one origin. The OBJECTID <= 1 AND OBJECTID >= 1 query expression definitely looked odd, so it was a good thought you had to test with more than one origin. Too bad that didn't end up being the issue.
Typically if there were a problem with one of the input parameters, the Make Feature Layer tool would generate a more specific error, like “ERROR 000732 Input Features: Dataset <blah> does not exist or is not supported” or “ERROR 000358: Invalid expression”. Your logs are showing that the tool returns “ERROR 000816: The tool is not valid”, which doesn't even make sense in this context. I sent a query to the person here at Esri who "owns" the Make Feature Layer tool. Maybe he can shed some light on what circumstances would cause the tool to return this error.
In the meantime, I think your best option is to revert back to using the slower ArcMap version. I'm so sorry!
One last thing to check on your end, if you haven't already: Can you run the Make Feature Layer tool on your origins at all, just normally within an ArcGIS Pro session? Does the tool work at all? If it doesn't, then at least we've found our issue. The best thing to do in that case is probably a) uninstall and reinstall Pro and try again, and if that doesn't help, call Esri Support and ask them why a core tool is not working on your machine.
Actually, for that matter, you could try uninstalling and reinstalling Pro anyway, just in case. Or hang on until Pro 2.9 is released in a week or two and see if that fixes it...?