Hello,
Let me try to clarify these doubts.

1) Root passive only effects 3 sword ninja, at its completely random. You can't chose who gets buff and who doesn't. Since there were 4 sword users, one of them didn't get buff. From your examples, it looks like they were kimimaro and mifune. (and yes, its a waste if bee gets the buff since he's already immune).

2) Those mystery's that are immune to interruption can't be stopped with interrupt skill/chase (Iruka/guy mystery or hashirama chase). But if they are releasing mystery, then that can be stopped with acuunture/immobile/chaos debuff.
But, if the 'interrupt-immune' mysterys gets root buff (Mifune, Hidan mystery) - then they can't be stopped with anything.

in short: Immune to interrupt mystery (Mifune, Hidan, Tendo) - Can be stopped with Acupunture/immobile/chaos.
Immune to interrupt+ Immune to debuff - Can't be stopped with acu/immo/chao mystery/chase.

Maybe it will be better if you bring 3 sword ninja only, that way it won't be upto rng then.

Hope it helps.:)