FPM can have per-domain memory limits which may override the system default. Check in /etc/php-fpm/domain-id.conf (I think Virtualmin has a UI for this, so you don’t have to know the domain ID, but I dunno where it is). If you see php_admin_value[memory_limit] that may be where it’s coming from.
I’m not sure if there are other places where it can be limited. I’m not very bright about a lot of PHP details, but I think we’re mostly doing things in the usual way you’d do them with FPM (I hope).
I know this isn’t the solution you’re looking for but I got so frustrated once that I did it. I just used the file explorer in Virtualmin and did a search for php.ini and changed the limits on all of them. (I had 4 at the time I did it.)
I know that’s not how it’s supposed to work, but it’s a sure fire solution.