From your description,
It sounds to me that the problem is in your PHP, not MySQL.
And, that would be entirely dependent on how your PHP website is written.
So, I don’t know that anyone can really help you, you’ll have to talk to your website coders/authors if possible, or dig into that part of your website yourself.
Or, if your situation is critical and/or beyond your expertise you may want to just roll back (BTRFS?)
The two websites in questions are standard open source packages Roundcube Mail and Word Press. I am not a php developer (I never went past C or shell script programming),
and I tend to agree with your assessment it may be dependent on the php, or maybe the apache mod_php module because connecting locally from the MySQL CLI works just fine.
Rolling back may be a problem because that was the first time I updated tumbleweed, so rolling back 1700+ patches would be equivalent to starting from the DVD distribution. However, I am considering the following two other options:
Falling back to a Leap distribution, which I have on a second machine and it works just fine with Word Press.