The lore works pretty much the same way as in many other zombie media. You can explain it to a certain point, but in the end it comes down to zombie magic to make it work.   As for the gap between the player and the character, I personally think that's one of the game's strong points. The lack of control in certain areas really helps build identity around your character, turning the sandbox into an almost story-like experience.

Beekeeping and bees should have been added a long time ago; furthermore, fish farming, horticulture, etc. are missing.

This is a very common issue in 42.19. I tried to throw a zombie into a trash can. A blank animation played, and the corpse suddenly came to life, started smashing the trash can, broke it, and then fell.

Microscopes fall through the table

I just though of this while driving over zombies. And noticed how literally stopping your car with a wheel on a zombies head doesn't do any damage which would realistically crush their head almost if not fully. And how you have to drive off of them and smack them again to deal damage.