Thanks for the thoughts, folks!
My idea isn't to have this as an issue that would present itself in every mission. In fact, I would like it to only be rarely, as a proverbial spice to the game, not a main ingredient. Ways to mitigate that could include gaining engine data, as I believe a few mods already utilize. This would mean you can't go for a deep interstellar mission with an untested engine without risking failure, but maybe with x amount of flights then the chance of failure is eventually eliminated, or the base failure chance is mitigated as you go up in tech tiers.
I think this should be an option in the game, much as reentry heating or permanent Kerbal death. In multiplayer it could be a server setting where the server pop all abides by the same rules. Sure modders can do it, but this gives players more options for re-playability in the base game. While there is a term, "Kerbal" denoting the inherent chaos in the game, the developers also did a great job capturing the spirit of astronavigation, physics, and aerodynamics. Some people crave a more realistic feeling to the classic KSP which is where mods like Realism Overhaul come into play. This would allow the game devs to optimize and market the game in another potentially profitable way if they add it as an option to base and not just allow it as a mod.