I don't know about you, but I use the Multi-Mod. I had the same end points, but no Mira ending option. So I sat down and held CTRL for an hour to skip through a fresh start and got the the very end again, whereupon I had the exact same Mira points but this time her ending was selectable. So yeah, probably some sort of bug carried over from an earlier version of the game and/or mod.
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If you want, I took that save and ZIP'd it up for you or anybody else who wants it. Again, this is a save made using the Multi-Mod, so make sure you have that installed as well, lest there be incompatibility issues. The save is at the last frame when The Cycle asks how you want to end the transmigration. Also, not for nothing, but the save is on page 138, slot 6 (cause that how many saves it takes to get to the end of the game when you save at every decision point). If you want, you can try renaming the file and just let it overwrite any existing saves if you find that easier.