CODE gets changed, and thus saves are nulified... it's not shit to do this it is normal when the game is in alpha. you might want to check your attitude about this, when games are being worked on the save data gets changed almost every update. after it's fully developed the fixes generally do not break saves unless there is something done to the save algorithm. If you don't like it so much, don't get every update, wait several or a large jump like .750 to .751. game saves didn't get broken till 7.5.7 after 7.5.0.
Most of the changes with the progression gates have very little to do with the save file. Adding a new object to the world? Save is irrelevant. Add a new variable that will get tracked in the save? Default it correctly and don't assume the save has the variable stored, easy. There was no need whatsoever to invalidate saves on literally every progression gate build.
There is a bare modicum of effort involved when you have paying customers, and derelict opted to ignore that and insult them instead. Those of us here who don't pay and complain are in a different boat, mind you, but derelict is making a minimum of $14k a month on patreon alone. Alpha builds or not, paying customers take precedence when reasonable measures can be put in place.
That said, the more recent updates regarding presets and breeding 100% needed save invalidation, because basic character structure handling was changed and writing a save converter is very different from putting in the minimum amount of effort required to not crash because an existing save is missing a new variable.