You could make your own boss script and allow a minimum time of 60 seconds if you’d like. The Training Dummy script allows fights down to 30 seconds if you want to use that one.
If you want to change one of the other scripts, go to the wiki: https://www.askmrrobot.com/wow/theory?spec=MonkWindwalker&version=live - you can expand the Bosses and pick the boss type you want to use. Click on that boss and then use the COPY button in the top center of the page to make your own copy of that script. Edit it and then change the minimum fight length.
As for what I consider a “real gain” in rotation development - I have a few rules of thumb that I go by. First, I see if what I am testing always results in a DPS gain. If it does, then it doesn’t matter if it is small, I’d consider it worth doing unless it is really complicated. If it is difficult/complicated, then I check how much of a gain it is. If the gain is very small - less than 1% - then I might not consider it worthwhile. Anything smaller than 1% is really questionable considering that simulation models are not perfect models of the game.
Another thing to keep in mind: Lets say you test 5 different rotation tweaks individually and find that each one gives a potential 0.75% DPS gain. If you then put all 5 of those things into one rotation and test that - you rarely would see a 3.75% DPS increase with all 5. The only way that would be true is if those rotation tweaks all had zero interaction with each other, which is almost never the case. This is why we use the method we do for testing rotation tweaks, and then we usually include an “overall” test as well to see what the sum total potential DPS increase is compared to just doing a bare bones rotation.
In the case of Windwalker and Touch of Death - during that 8 second window you essentially get 10% increased damage on any ability you use. If, for example, you hold FoF for a few gcds to let it happen during ToD - and then end up using FoF one less time in the fight - you lose way more than 10% of the damage of a FoF. Even missing one tick of a FoF would not be worth it. If you have to use a BoK while you are holding FoF, you lose out on the CDR from that BoK - so the opportunity cost of holding abilities as a WW is generally too high to make it worth it in the long run. You’d be looking to instead delay ToD for FoF, instead of the other way around. I’ll test out some logic for trying to sync a SEF with ToD as part of the tests I do.