My son had a 99 YZ125... When we purchased it, the top end had 20 hours of racing on it. He road it for several years on both woods and track (no racing). As time passed the took over my 250 and I sold the 125 to a buddy. He wad beat the piss out of that bike... little to no maintenance. He rode it for years knowing it needed a top end, but continued to ride it. the water pump seal failed and he limped home for the woods with an overheating bike. He parked it and life got in the way... it sat for 18 months, after me prodding him to get it out and fix it, he pulled it out of his basement, kicked it 5 time it fired up and he rode it onto my trailer.
When we tore it down, the internals were in excellent shape... Other then being filthy dirty, everything was pretty good. Yes the water pump seal was bad, the piston was way past due, but the cylinder was in excellent condition (I guess all the blow-by helped coat the cylinder). The rod was tight, and the crank bearings had no play that I could tell. We put in a new top end, new gaskets, new water pump and seals and she still live today..
I guess the moral to my long winded story is yes a 125 needs a little more top end maintenance, but I think the crazy maintenance routines of some riders are a bit much. Some seem to enjoy wrenching more then they do riding. You should be able to go 100 hours on a top end, and 250 - 300 hours before thinking there's a bottom end issue. To answer your question "Are these YZ's really that lightly built, or are people doing a lot of unnecessary work?" I feel they are doing unnecessary work.