Very true, which reminds me of the Doctor/Master phonecall when they talked about the Time War and the Master confessed to running in the end. Becoming Yana was about hiding, yes, but in a way self annhilation which was what the Doctor was doing/expecting to happen when he ended the war the first time around as well. (Not just in the sense of suicide but in the sense of destroying who you were.)

re: the ship teasing, in addition to all the overt stuff in The Bekdel Test, the bit in Animal Instinct when River told Crispy that for all his penchant of laying traps for the Doctor "I married him - try and beat that", it cracked me up as well. In the Extremis flashback Missy comes across as sincere, not taunting, when she gives the Doctor her condolences re: River, so that ties with River and Missy parting on reasonable (for Missy) good terms.