These timer problems are due to a lack of foresight from the original programmers of SCI. There are a lot of other games from around the same time that do not have speed problems even when running on blindingly fast PC’s.
They could’ve made timer based puzzles run off the screen refresh rate (60-70 hertz in most cases ever since CGA was around) or the internal clock of the PC. These were extremely common techniques that a lot of other developers were using back in the 80’s and 90’s. This would’ve future proofed their code for decades and there would be none of these timer related bugs that everyone has to struggle with now.