Maybe it's not a consideration, but will the Permatex "glue" the fan to the pit making it difficult to replace?
Perhaps you could put waxed paper on the pit then run the Permatex bead on the fan and bolt it in place. When the Permatex is set up (and "glued" to the fan), remove the fan and discard the waxed paper. That might leave an exact gasket on the fan.