There isn't a special reason. I usually do it this way with cerbot - once - for 8 second level domains.

I see. Does certbot read the paths from Apache or does it ask you to provide a seperate path for each of the host names? Something like the latter can be done with simple-acme using global validation settings, though that will not really make the amount of configuration work required less.

When I use "certbot" to renew certificates, I manually launch a command. It gives me the name of each validation file and its string content. So I manually prepare all the files and put them in the relative different directories. The program proceeds with the validation process and generates a single certificate.

I've created a feature request for this on your behalf: #42

You can currently to this if you pick DNS validation, but then you'd be creating DNS records instead of working with files. But generally you'll want to have the renewal process fully automated.