Well, everyone is gonna have a different opinion on this stuff, but... No miss/no bombs is the main thing, and I think border breaks/tranced runs should not be included, while those that use UFOs may be (for now) since the only one we have right now only used UFO's for scoring, not for free screen clears, which only made the run harder to complete.
On the other hand, I don't see a reason why a run that timed something out shouldn't be included. The "perfect" mindset is flawed when it comes to this, It's a western thing which people have used to apply to stage practice runs, not to full runs. Applying this standard that nothing can be timed out to a full game run where some attacks will inevitably be timed out from time to time due to RNG making it impossible to capture... is not quite fair.
Then again, how these anomalies are noted isn't important to me. If you're not gonna add the NBNT to the list, it does still deserve to be noted somehow, which is why I think it would be interesting to add a "close calls" section at the bottom for those ridiculously close runs. Of course, this may be turn a bit arbitrary...