Is it do-able, or will we still have to modify the .php config file (which really isn't a big deal)?
The SME "paradigm" is that the behaviour of the system is completely specified by the configuration database contents and the set of configuration file templates. If you modify any of the config files by hand, or by using an application (e.g. webmin, or the webmail admin interface), then you break this paradigm, so you cannot, for instance, restore from backup and have the same configuration.
The webmail admin interface is therefore hidden, and will likely remain hidden (unless someone modifies the admin interface so that it updates the SME configuration database when you make changes).
So, continue to change the config .php files, but do it by providing custom template fragments.