I am using Workflows and Rules to build a custom project management software. My system has a content type "Tasks". Task nodes have a field "assigned to." I have rules to change the value of task.assigned_to based on the workflow status. I discovered a way to edit the workflow comment for these rules. I use the following action type "Custom PHP code":

 //IMPORTANT: DONT USE PHP TAGS IN THE RULES ACTION!
// Generic
$node->workflow_comment = 'Your message here';
// Specific example
$node->workflow_comment = 'Task [node:title] reassigned to <a href="[site:url]user/[node:field-manager]">[node:field-manager]</a> (Manager)';

I am not sure if this is the best way but it worked for me. If anyone knows a better way, pls feel free to tell me. Hope this helps!