By default, php's opcache only stores 2000 files. That's likely not enough, I have around 12000 in one of my medium-sized projects.
You can configure it and set it up to 100000. You can read more about tweaking it here: https://tideways.io/profiler/blog/fine-tune-your-opcache-configuration-to-avoid-caching-suprises

What about a self-check that outputs a warning if we have the default setting? I mean, your setup is not broken at all but you can get a huge performance gain if you optimize this.
The manager could even propose a good value by counting the files and rounding up to the next 5000 step.

$ find ./ -iname *.php|wc -l

Wdyt?