I think the CD-R problem has two main aspects:
1: getting the laser stuck past it's ability to bring itself back. This is a defect in the design (shouldn't be possible, but is) and is easily fixed.
2: CD-Rs require more work from the PCE to read, and hasten the death of lasers. The shit was 15-20 years old already, you just put the final nail in the coffin. Everything dies, that's the way it goes. By a time an Xbox 360 is 20 years old it will have need to have been rebuilt 12-15 times, from what I can see, so the PCE is a real champ.
I've only spent a decent amount of time on two CD-Rs; the translated Y's IV, and a remix I did of LoT. I had read problems once in a while, more than retail games, but it wasn't that bad. So in moderation I think its fine. If a CD-R kills your system instantly, it must have been pretty far gone.
So have a spare HOP3 laying around, and avoid CD-Rs as much as possible.