The end game strategy can make quite a difference, perhaps 10%. Finding the exact time a script should start buying provinces is troublesome, so just making sure there is some gold in the deck is a shortcut. Getting the number of provinces left in the supply to start buying duchies is quick. Just try out a few value. For colony games use "buys/gains needed to end the game" instead of "colonies remaining in supply" and make sure the duchies are not bought too soon.
A simulator bot will have no concept of a three pile ending unless you script it, so the bots will buy out supply piles when they're behind and ignore ways to close out games when they're ahead. Unfortunately you can only customize the script effectively when you know the competing bots and know which piles will be emptied. Aside from 3 pile endings, there are some times when a badly losing deck can stop buying provinces and buy platinum to push for a win on colonies. Variable vp cards nearly always need special conditions.
I'll also suggest that all scripts always have access the same vp cards, so that if you're testing a tunnel strategy against a big money baseline then the baseline can buy tunnels too. It makes a significant difference. The same can also be said for kingdom card treasures.
if I use a very simple endgame strategy for a custom bot and a baseline opponent, will the simulator lead me astray in determining whether the custom bot is at least a viable strategy?
Not really. The worst case would be when you miss games ending on cheaper vp cards, perhaps duchy, estate, and curse. There are plenty of kingdom cards that make a difference but hopefully you can spot them - treasury, rabble, hoard, etc. Engine decks need watching carefully since too many green cards can kill a deck entirely. If you're checking there is gold in the deck before buying a province then make sure the bot will buy the gold and not be stuck on banks or wharves instead.