Electrical – How to protect non-metallic cable parallel to face of joist in attic

The answer to your first question is YES. You need to have the junction in a box. Can you mount the box higher on the roof or a rafter or a gable end stud? if you don't have enough wire, then practically speaking, the box will have to live under the insulation. Technically it is not enclosed as in being sheetrocked over, so it is not a code violation in an older house. but when you do bring out the new wire, be sure it appears above the insulation before you go back down into a wall. you could also tag the wire with a label.

The answer to question two is very simple. You do not need to run NM cable (Romex) in a conduit in a residential framed wall. You also do not need to secure fished wire except in the actual devise box entry hole.

I’m not a NEC attorney nor did I stay in that fancy motel last night but one of the “intents” of “the rules” is to reduce the number of material casualties suffered during construction. A sheetrock craftsman won’t use 16-penny nails to mount sheetrock and is highly unlikely to miss the studs or furring strip with a standard drywall nail or screw, hence the 1 1/4” (and metal plates) rules. Mr. Homeowner, while installing a shelving unit for knickknacks might use a 16-penny nail but I’m confident wiring a house with EMT would turn expensive in a hurry.