Is it possible to make blueprint with merged chest normally rotatable?
Maybe using rect of linked chests instead of entity-per-size? (Performance +- same if i checked it right)

Chests not being rotatable is limitation of the game. It might be possible to modify blueprints just after they are created to split any merged chest. That way the blueprint would be rotatable, but you would have to merge the chests after blueprint is placed again.

Using linked chests instead of merging them would be completely different mod. It could work similarily that you place down entities and then link them with some selection tool.

Are you sure it is still a limitation? Elevated rail foundations change shape when rotating, so it stands to reason there should be a way to link NxM and MxN variants as rotations.

Yes, it is not a question of whenever the entity is rectangle or not. It it specifically mentioned in the docs: https://lua-api.factorio.com/latest/prototypes/ContainerPrototype.html : A generic container, such as a chest. Cannot be rotated.

Couple of possible solutions were suggested to developers but apperently they didn't like any of them.