I believe that's why you don't use the most extreme thought experiment and then go "okay, thanks, we're done here". You want to be able to zero in on different factors. E.g. save the musician by giving five minutes instead of nine months? Lower the risk of death of a part of society by accepting some restrictions on your freedoms?
I view it like a black box where you can define inputs and observe the output and your goal is to understand what calculations are made inside. Thought experiments are essentially fuzzing it to understand what's happening. "What if it's a fat guy? What if it's a smoker? What if it's a politician? What if it's a homeless person? What if there are 10 people, what if there are a million?" and you're iterating over lots of options to get closer to understanding the formula.
After all, a thought experiment that only holds true given an impossible premise would have no rhetorical power if we weren't willing to extrapolate our conclusions beyond the premise, to the possible. Which we are - that's why the trolley problem is taught to people who aren't railway signalmen.
There's a risk there are arguments we think are convincing us because they have isolated a pure abstraction - but actually it's the false dilemma in the premise that convinced us, while the argument distracted us.