How to cover the attic rafter bays after installing baffles from the soffit before replacing the siding

I am sorry but this sounds like horrible advice. Rigid or spray foam should not be used in large attics unless you just have money to burn. For your $ fiberglass blown in insulation is perfect for your installation plus plywood. (Fiberglass over cellulose since insects may love the coziness of the "wood boxes").

Also in large attics you ONLY insulate near the top floor ceiling. Insulating the roofline is useless.

You're asking two questions:

Is it ok?
Yes, it's ok. There's no substantial difference between the resulting fiberglass batt and a new, unfaced batt aside from marginally less fiberglass due to what pulls off with the paper. The batts may want to pull out as you remove the paper, so it might make sense to simply do it on the floor and reinstall backward so you have a cleaner face exposed to the room.

Is it necessary?
Your plan is sound: Don't have more than one vapor barrier.