As of Sakai 2.4.0 release, OOTB Sakai set default permission for mailtool. Instructor (in a Course site) and Maintain (in a Project site) has proper authorizations to use Mailtool without extra setup.
Turn on the Mailtool permissions (mailtool.admin and mailtool.send) via !site.helper realm
Two permissions are defined for permission-based Mailtool. It should be turned on before Mailtool is added to any site. Existing sites may need to turn on the permission via !site.helper realm (note: OOTB sakai has just one role in !site.help: maintain. In order to turn on the permissions for this role, click "maintain" and then check the boxes next to mailtool.admin and mailtool.send. That means "maintain" role will be allowed to send emails using Mailtool and be able to see/change defaults in options page.
Check updated JIRAs about this issue
Common case scenarios
e.g. per course type site, Instructor role will have both permissions. Teaching Assistant(s) will be allowed to send only.
In order to turn on the Mailtool permissions for other roles, use "copy role" link. Click "maintain" and click "Copy role" and then type the name of role you want(e.g. Instructor). It will copy all permission of maintain as the name you typed. Check the boxes next to mailtool.admin and mailtool.send. (If you already checked the boxes in maintain before, it already were checked)
Repeat this procedure for other roles (e.g. Teaching Assistant. you may want not to allow "mailtool.admin" permission to TA. In that case, uncheck the box next to mailtool.admin in Teaching Assistant after copying the role from Instructor or maintain)