(instead of based on uri or vhost)

FCGIDCommand /path/to/command
  IdleTimeout n
  MaxProcessLifetime n
  MinProcesses n
  MaxProcesses n
  MaxRequestsPerProcess n
  InitialEnv var[=val] ...
  <class>

(the names of these options follow my proposal for the names of existing directives ;) )

When a command is to be started by mod_fcgid, any options specified for the command on this directive override those defined for the uri, vhost, global, or the defaults.  When a wrapper is used, it is that wrapper which must be specified on this directive.  This directive is not required unless one or more options must be customized for a command.

Initially this would be allowed only in global sections.
InitialEnv can be repeated.

Regarding *class*:  Something is needed to disable or alter existing management of applications based on their class.  Currently a class is limited to the processes started by the same command within the same vhost (except when ServerName isn't specified) with the same identity.

One possibility is to provide an option to ignore the vhost name when managing the class (IgnoreVHost or ClassIsGlobal).  Another possibility is to set the name of the class to be used in lieu of the virtual host (ClassName foo), which could be used to the same effect but might be more useful in the future when the process manager can see per-server configs (for existing directives as well as FCGIDCommand).

None of this would affect the identity checks.  (Processes with different uid/gid would never be considered to be in the same class.)