Well, it doesn't like the new httpd command, either, so go figure. CentOS Stream 9 isn't a workalike to CentOS 7 (which I had before). New distro, new commands, and new ways ... that's where I think the biggest part of the issue is.
Oddly, that isn't what fixed it, though that was additional clues and such ... ultimately, this was just my reluctance to show my work (e.g., show the actual, full command).
What I hadn't considered was that the sort order from multiple directories has to match up exactly with the sort order from multiple domains. It's getting confused because www.* is an alias for the main domain, and so it's counting that as an extra subdomain (throwing off the counts and mis-ordering the files it's trying to drop).
So, adding a SECOND instance of the correct directory (e.g., identical -w for each -d alias) to align with the alias (rather than just adding the domain by itself) worked perfectly.
What worked:
certbot certonly --webroot -w /path/to/primary/domain -d example.com -w /path/to/primary/domain -d www.example.com -w /path/to/subdomain_1 -d sub1.example.com -w /path/to/subdomain_2 -d sub2.example.com -w /path/to/subdomain_3 -d sub3.example.com