I would always record all of the zeros so that your power curve doesn’t get skewed towards over estimating your abilities.
Imaging a scenario where you’re doing intervals at 110% of FTP, say 8 minutes on 3 minutes off and resting completely between work bouts with zeros not recorded. If you did 5 of these that would show up as an average power of 110% FTP for 40 minutes, when the reality is that you only averaged 84% of FTP for 52 minutes.
Normalized power get affected on the same basis.
I’m pretty sure TR doesn’t add zeros back when they calculate the metrics and they’ve state on the podcast that you should always have zeros recorded.
It’s also recommended not to use smart recording.
Mike