THAT paper makes alot of sense, and I've referenced it many years ago when designing outside broadcast gear.
INA163 datasheet Fig.5 runs the risk of damaging the the 1N4148's (see THAT paper) if there is a sudden short to ground - they aren't great diodes for pulse applications. I think you'll find experienced audio designers are likely to use something beefier with an INA163 (assuming they can afford to design one in - pro audio BOM's are TIGHT), or fitting series (Rs) resistors.
Answers:
1) When not using phantom power, there will be no overall bias on the electrolytics and they will be subject to reverse voltages. If just a microphone levels then not really a real-world problem - but if the front end is designed to also take line levels, then there could be (+12dBV is 11Vpp) substantial reversing taking place. If you are bothered, put two 100uF series back-back.
2) 48V Phantom is +48V w.r.t system 0V, not -48V.