The shift shaft seal should not pop out of the seal carrier. If it does, someone did not loc-tite it in properly. Most, even Mercury, use to say not to use loc-tite on the outside of a seal that is rubber on the outside like a shift shaft seal. If loc-tite is not used on that seal, then it will pop out.
It is a single lip seal designed to purge oil past the shaft seal lip, not pop out.
I didn't mention the part about draining an ounce or so out after filling since most, including myself, will loose that much lube while installing the lower plug into the carrier anyway.