There are some instances where maps don't have a motivator included (dr_cocainum, dr_safety_first - but the timer almost never reaches the end - ; dr_wintervalley_final - the spawn stalling with at least 2 medics healing each other - ; some pre-2016 maps; etc.) , so the timer is the only "salvation" for the round itself when there are people who stall, wether it's intentional or not, going at a slower pace or they're afk.
I agree that dr_simulacrum and dr_cybertower_v4 (very rarely reached end of timer) and very few couple of maps have a problem about the timer, due to the fact that a person who reached the end of the map has to either wait until the timer is close to the end, so that he can sacrifice and respawn the others for the said minigame / boss, or simply go for it and try to finish the minigame in time.
There were a couple of suggestions said in the server about a vote system that would either extend the timer by 5/10 minutes or simply eliminate the timer for the rest of the duration of the map, but I haven't seen any suggestions made in the forums.