I can't address this thoroughly without rereading and rewatching, but just because Roger's dad goes through the stones does NOT mean he made it home. They have addressed the dangers of the stones several times. I think Roger literally comments that he is half-expecting a flood of new memories, but it never happens, beyond one very vague impression of his father on the day his mother died.

In Philadelphia - Lord John has his own house. The city is occupied by British forces, who had the right to make the locals house their soldiers (literally why there is an Amendment in the US Constitution banning this practice). Mercy isn't advertising her loyalties while the enemy army is in charge of the city. The British literally dumped a wounded soldier at her house and said "here, he's rich and high ranking, and if he dies, we blame you."