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Ended up buying the fully upgrade all weapons, pods and all endings achievements at the resistance camp which isn't nearly as expensive as you'd think (about 300,000 in total for all 3) just to skip the grind. Also, I think a lot of the extra endings take away from some of the greatest moments of the game and ruin the pacing and tone (replaying 2B's run to the bridge being the worst instance) so I'd probably recommend to all to buy that achievement and not grind them out in gameplay as they're all the same "and so the character decided to just go the other way for no reason" bar a few.
I noticed that in route B we have to jump to 2 chests which are quite far away (Archive #9 and #23). As 9S it's actually easier to take control of a small flyer and just fly over there and then to self destruct to get back out.
Might be worth mentioning as an alternative way to get there.
Lastly of course, there is the special "Achievement Shop" in Route C that you can always buy your Steam Achievements, but that isn't necessary. Only if you wanted to skip the Material grinding basically.
Actually, I just got far enough through Route B and saw Father Servo in his final form on the roof minutes ago. So I figured some of the quests do restart where they were left off during Route A.
Appreciate your feedback!
But yes, though the Missile Supply will fail those two, all Sub Quests essentially restart in Route B so you get a second chance at completing any you may have missed. You can also repeat previously completed ones, but they only count once for the Mercenary Achievement.