Very good points. I haven't really thought about it since I only had the opportunity to complete parkours other than the ones you mentioned (Chillroom, City). Afterwards, parkour went into maintenance and was closed down.
It would definitely be more benefitial to have a saving system rather than a timing system. Idealy, you would have both working together, but if there's no other option, I would rather have the saving checkpoints plugin atleast on Chillroom and City.
I understand that the whole server is a WIP, but, again, your thread is a major factor in the future development of parkour which should be considered.