Please don’t hijack posts that are not identical to your problems. See fourth bullet point.
As an update to my problems, I wiped everything (files & db) and tried using just 3.4. This has the same problem, which just convinces me further that the problem is within my setup.
I ended up stumbling upon this post. I am using Apache virtual hosts so I added the options listed. However this did not change anything.
So I jumped over to my test virtual host and repeated the whole fresh setup of 3.4.1. Guess what, the ‘chris’ sub-directory site works. This means the problem is definitely in my virtual host config for https://www.theclonchs.com.