Is there a drush command to set permissions to true on ALL modules for administrator?
You need to look this Permissions API

$ drush help perm-grant
Grant permissions to a role.

Examples:
drush perm-grant --roles="Admin"          Grant all permissions provided by the Node module to the Admin role.
--modules="node"                                                                                              
drush perm-grant --all-modules            Grant all permissions to Admin role.                                
--roles-="Admin"                                                                                              
drush perm-grant --roles="Editor,Copy     Grant "administer nodes" to Editor and Copy Editor roles.           
Editor" --permissions="administer nodes"                                                                      
drush perm-grant --all-roles              Grant "administer nodes" permission to all roles.                   
--permissions="administer nodes"                                                                              


Options:
--all-roles                               Grant the permissions to all defined roles.                     
--roles                                   Comma-separated list of roles to grant permissions to.          
--permissions                             Comma-separated list of permissions to grant to a role or roles.
--modules                                 Comma-separated list of modules providing permissions to grant. 
--all-modules                             Grant all defined permissions to a role or roles.  

$ drush help perm-revoke
Revoke permissions from a role.

Examples:
drush perm-revoke --roles="Admin"         Revoke all permissions provided by the Node module from the Admin role.
--modules="node"                                                                                                 
drush perm-revoke --all-modules           Revoke all permissions from the Admin role.                            
--roles-="Admin"                                                                                                 
drush perm-revoke --roles="Editor,Copy    Revoke "administer nodes" from the Editor and Copy Editor roles.       
Editor" --permissions="administer nodes"                                                                         
drush perm-revoke --all-roles             Revoke "administer nodes" permission from all roles.                   
--permissions="administer nodes"                                                                                 
drush perm-revoke --reset                 Revoke all permissions from all roles.  Requires confirmation, use with
                                           caution.                                                               


Options:
--all-roles                               Revoke the permissions from all defined roles.                        
--roles                                   Comma-separated list of roles to revoke permissions from.             
--permissions                             Comma-separated list of permissions to revoke from a role or roles.   
--modules                                 Comma-separated list of modules providing permissions to revoke.      
--all-modules                             Revoke all defined permissions from a role or roles.                  
--reset                                   Revoke all defined permissions from all roles.  Requires confirmation,
                                           use with caution.