Ye I already planned to adjust these objectives, should be reworked in the upcoming 0.6 release :)
I will say, (speaking as a playtester of sorts) that the times I typically get when playing good have constantly been twice the estimated time.
it also seems a bit off-balanced with there being so many relics and consumables that help you with reducing click count and not taking damage, (and I'll even count the radar as helping you go flagless, since it doesn't actually count as "using flags"), but pretty much only a single relic that helps you save time.
I mean they don't need to be equally available, just that there should be strategies that make any singular one of them easy in the late game (they can even still be mutually exclusive, it's just that ).
you could also just make it an accessibility feature in the settings, since probably 60-80% of people would find the time goal to be just right, and that it would be too easy for such people if you lowered it (it would be an honor-type system though, in terms of people not using it when they don't need it, but I think people would respect it, kinda like assist mode giving you extra life in Mario odessy)
timing is a notoriously hard thing to adjust for, because you don't know how long people will take on each step while thinking about things, especially on as short of a timescale you have here. The times it does work are usually when a predictable, repreatable interation is initated by the player, allowing them to take the time they need to adjust to it.