Are there any places, reasons, etc. where I may lose time compared to an NES or Emulator, due to using an NES Classic?

Even if your run is retimed with bowser patterns the time will still be converted to NES classic framerate. (You will lose ~0.5 during a 5 minute run)

The NES Classic runs at exactly 60 fps while the normal NES and emulators run at ~60.098 fps, so like the answer above says you will lose about half a second every 5 minutes. It's not a huge deal until you're getting to low 5:0X times so don't worry about it too much