I think Shacks has nailed the salient point here. Most ballast and other work trains operate during track possessions that coincide with isolation of the overhead. Even if having the overhead energised was not a problem for other disciplines working in the same area there is the problem of alignment of the track with the wire. Newly laid (or relaid) track just gets whacked down as close as possible to the intended alignment. Then it gets ballasted and then the tampers, regulators and dynamic stabilizers came and jiggle the track into it's final position. I remember being told that a misalignment in the track of an inch can give a six inch error in the position of the pantograph. Having electric loco's operating on new roughly laid track would be asking for trouble.
Also if you were operating electrics in a close down environment you need to consider the traction return current through the rails. You have to have a good continuous connection through the rails back to the sub station. With rails getting cut and welded you would have to have the signal electricians doing a lot of bonding around any breaks in the rails or someone will get fried big time when the electric loco's try to move.
In the situation mentioned with the track laying in the NSR, there would have been no overhead wires or electrical infrastructure to support electric loco's on work trains.
Using the 86's for jobs in tunnels where the track and overhead are intact is definitely the way to go. There will always be situations though that preclude electric traction so there needs to be a safe alternative.
I agree that the scrubber fitted 48's are probably as bad or worse than some other diesels for tunnel work. The lovable but decidedly low tech Alco donk probably makes many times more pollutants than a newer, cleaner design of diesel would. Even allowing for the scrubber a loco like an NR would probably be cleaner to work with in a tunnel than a 48.
If Workcover ever decides to investigate the air quality in the tunnels on a shutdown with the 48's operating I reckon you might see them banned or see the crews issued with proper breathing apparatus. The fume levels would have to be illegal on some of the work sites I've seen. Maybe someone should make a phone call next time the 48's are down the tunnels?