The sealer I used is just the Permatex Ultra Grey RTV. It has a smoother and less sticky consistency than red, for example, and is easy to "smear". As I recall, the shaft should be back from the face of the case a little bit, so if you get it clean and dry you should just be able to put some of the RTV on a body putty spreader and smear it into the recess.
There used to be a guy who sold rebuild kits under the name Toploader Heaven and he had a very nice and comprehensive set of illustrated instructions for use by the novice rebuilder. His instructions included a recommendation that this area be sealed with RTV or I probably wouldn't have thought to do it.