Yeah I think the extended version of the Phasma duel should be included to better justify its own existence. As you say, it very well could lead into the mass desertion themes of your TROS book edit.

Maybe you could omit some minor details, like Phasma’s hand getting choped off or the whoop-hog line. But overall the scene should be there, with greater focus on the stormtroopers’s choice.

I haven’t read the TLJ novel, so is there the deleted scene with Finn and co. meet some stormtroopers inside an elevator? In that case you could tie both moments together, maybe having the trooper that talks with Finn being the first to point his gun at Phasma.