No problem. This lead me down another path.
Instead of having a separate file or modifying the interworx generated config file, I tried putting the config option directly in the main php-fpm config (www.conf) as:
[example.com]
php_admin_value[memory_limit] = 256M
Not completely ideal. The main issue being that if the siteworx is deleted, PHP will fail to start (confirmed). But it does work.
Also, of note: it doesn’t seem like the ~/etc/php.ini (or ~/etc/php-fpm.d/example.com.conf or anything else I tried) file is loaded by php-fpm. And putting values in the .htaccess doesn’t work either (causes Internal Server error because php is already running).
So, thanks for pointing me in the right direction. If you have any other better ideas, I’d love to hear them.