It's just how things get over time, people will take out something others may consider fun, to instead boost performance. Really an inevitable optimization, as something like this could have been done by human testing and external logging, instead of an external tool to simulate attempts.
In regards specifically to Trackmania, the best solution to my mind is to split the leaderboard between analogue inputs and keyboard. I know that's basically letting the program win, but it exists now, and unless they introduce random physics or performance, the door can't really be shut.
In terms of speed running, this has also been done in other games, such as TAS runs or the AI they used in SMP64 to find new strats. I don't really seeing it going away, even if it makes runs less bespoke and more like generic IKEA furniture.
