Please disregard. Issue turns out to be a masterlist bug, rather than a design oversight.
This is not a user-friendly setup. I like the "conflict resolution" minigame that you have, click the link to remove the conflict etc. It's neat.
Entry users, however, are going to be utterly lost when it comes to plugin sorting. Especially as Vortex overrides LOOT/Bash sorting, requiring autosort to be turned off so that manual sorting can be enacted.
Such as above, where you don't want Maskar's ahead of Bashed.