For a single application, it's not too bad. When you have dozens of applications that all have different mechanisms to install a CA, rotate certs, etc. And some of those don't have a good way to automate rotating the certs, then it becomes a pain.
I don't think so. We run a horde of machines, and run plethora of services, which are custom and/or has a very narrow install base due to the niche they serve.
99% of them use system-wide PKI store for CA and their certificates, which is under /etc. All of them have configuration options for these folders, and have short certificate lives because of the operational regulations we have in place.
At worst case, we distribute them with saltstack. Otherwise we just use scp, maybe a small wrapper script. Managing them doesn't take any measurable time for us.
> 99% of them use system-wide PKI store for CA and their certificates, which is under /etc.
Consider yourself lucky then.
For self-hosted third party software, I've seen requirements to provide it in an environment variable, upload it to a web form over plain http on localhost, specify an AWS secret service secret that contains it, put it in a specific location that is bind mounted into a container, create a custom image (both VM and container), etc.