Using “Unlock all Techology inside Sandboxes” unlocks all science related achievements.
Before Space age this setting had no effect on them.
Is this how the game works now or is it something that should be fixed?

I don't know if the game previously had achievements relating to science packs, but this mod doesn't do anything relating to achievements; it has always been possible to trigger them within the sandboxes, and as far as I know there's no way to control that. You are, after all, doing those things, and there's no way to tell the game you aren't doing something that it knows you're doing.

I know that it's slightly better now given that production statistics are somewhat per-surface, but for example you can still reach rate/total limits for production within the sandboxes and get the achievements for them.

I guess I'll have to adjust to that. Until I discover all technology myself. Thanks for the info.