Re: Lower seal
One reason for the inner seal facing in is that the gearcase is sealed. Even though when filling there is a slight unavoidable air gap, it could still build up pressure. Additionally, the gears in there are rotating at high speed (2500 rpm for a 2:1 gearbox at engine rpms of 5000). Any pressure from the outside would be slight as there is no mechanism to cause it to be much of anything. Water pressure is 1/2 psi per vertical ft. Running in F gear actually has a vacuuming effect mitigated by exhaust gasses. Possibly R could put some pressure on it but the prop is in the way.
For me, common sense prevails and I agree with my manual. Additionally, as I recall, these seals come with a spring around them which helps them to stay put even when worn.
My 2c,
Mark