We don't judge a player based on progression here.
To answer your questions,
1) Yes, the mana cost outweighs the benefits.
2) If your atonement is too late, then you were too slow. However if your group has strong spot healers (like a resto druid) then I honestly wouldn't worry about them and save your mana. I personally keep PW: S on CD, always good to throw on the tank.
3) It's better imo to let it drop and just prep for atonement healing. You're making the right choice.
4) I've seen some wild answers out there in regard to this, I don't have it so I can't give you an answer on that.
5) I think total has a trinket list floating around somewhere.
6) The fact that you understand that Flintoid's healing method is flawed and that his logs are skewed should answer that. It's not exactly viable, but at the same time if it's what your raid needs you to do, do it. Since you have strong spot healers already, this won't be an issue for you and you should stick with prepping atonements and healing in bursts.
7) That DPS is very low for a mythic +, it sounds like you hit the wall as a group. As shadow I pull ~220k DPS and I'm usually 2nd or 3rd DPS on serpent, and 350k+ on wrath (execute fight FTW). For mythic dungeons your healing style will be completely different from what you do in a raid. Essentially you'll be spamming Shadowmend to keep people topped off and DPS when you can. It helps loads if you spec into grace and ToF as it can boost your healing when you really need it. I think you could push higher in mythics, just have to adjust some talents and healing style.
Also as a tip, turn off your healing meter if you have one, especially for raids. If at the end of the fight you killed the boss and no one died due to a lack of healing, you did your job. Use a website like WCL and post here to see how you can heal better, but you have more important things to worry about mid pull.