These PHP apps need to change so you first boot the app with credentials so the app is secured at all moments.
The reason for this distinction is that failing to meet a Requirement for issued certificates would mean the trust stores might remove your CA, but several CAs today do issue unlogged certificates - and if you wanted to use those on a web server you would need to go log them and staple the proofs to your certs in the server configuration.
Most of the rules (the "Baseline Requirements" or BRs) are requirements and must be followed for all issued certificates, but the rule about logging deliberately doesn't work that way. The BRs do require that a CA can show us - if asked - everything about the certificates they issued, and these days for most CAs that's easiest accomplished by just providing links to the logs e.g. via crt.sh -- but that requirement could also be fulfilled by handing over a PDF or an Excel sheet or something.
LetsEncrypt doesn't make a difference at all.
FWIW - it’s made of people
You meant you shouldn't right? Partially exactly for the reasons you stated later in the same sentence.
CA/B Forum policy requires every CA to publish every issued certificate in the CT logs.
So if you want a TLS certificate that's trusted by browsers, the domain name has to be published to the world, and it doesn't matter where you got your certificate, you are going to start getting requests from automated vulnerability scanners looking to exploit poorly configured or un-updated software.
Wildcards are used to work around this, since what gets published is *.example.com instead of nas.example.com, super-secret-docs.example.com, etc — but as this article shows, there are other ways that your domain name can leak.
So yes, you should use Let's Encrypt, since paying for a cert from some other CA does nothing useful.
They don't sell who asked because that's a regulatory nightmare they don't want, but they sell the list of names because it's valuable.
You might buy this because you're a bad guy (reputable sellers won't sell to you but that's easy to circumvent), because you're a more-or-less legit outfit looking for problems you can sell back to the person who has the problem, or even just for market research. Yes, some customers who own example.com and are using ZQF brand HR software won't name the server zqf.example.com but a lot of them will and so you can measure that.
I am not entirely aware what LE does differently, but we had very clear observation in the past about it.