Helicopter tape can protect the bike tubing. As to bags wearing through, that’s the cost of lightweight, if the bag can move when you hit some rough stuff. The old canvas bags and rolls strapped on in late 19th and early 20th centuries would stand up to the abuse, at the cost of weight.
Ordinarily yes, however, on my Kona there is a metal head badge with some very sharp edges and helicopter tape wouldn't help much there, hence the plumbers insulation.
Another issue I have with bike packing setups is capacity. Id struggle to carry enough for a long weekend ina bike packing setups without spending serious money on getting really lightweight gear.
Also that of stability. Panniers place weight lower down where the bikes handing isn't as affected. The big seatbag and handle bar affect the rear and the steering of the bike.
Personally I think one causes the other. When I rode my Slovenia trip, I was carrying some old, not terribly small or lightweight kit that also wasn't well packed. The handling as a result was interesting, however these days I have smaller, lighter kit that has resulted in the bike being much better packed. All of the weight is spread around the middle of the bike and the handling not that different to how it is unloaded. I have certainly tackled some interesting off-road sections with lots of confidence and no problems with the bags upsetting the handling.
Interestingly this year I've already completed two trips with folk who where using a two pannier set up and on the routes we were completing they both struggled with all of the weight being biased to the rear of the bike and making the front too light, whereas my bike felt quite neutral in it's handling.
Money is definitely a big problem with all of this though, especially if a pannier/rack set up works for you. Personally I've saved some money where I can by going the Alpkit/
Decathlon route where I can. Alpkit for example make some great equipment at really good prices and back it up with some great after sales service.