Part of the description states that where should be no looking for bosses or exploration but this is not set as rule.

Would this be seen as bad if player had option to enter one of 3 rooms where room A has a blockade that he can't overcome. Room B would bi locked. Room C would contain Boss that will give powerup that will let me remove the blockade from room A and show me the new powerup in action. And after blockade is removed I get the key that unlocks Room B where I meet the next boss.

Each boss would keep giving player new powerups that expand its capabilities (like double jump, roll and so on) but I feel player needs to learn about them somwhere before facing boss that requires them to have it.

So is it ok if we have some transition and story rooms? And is it ok if they are placed in non-linear order?

It is fine to have things inbetween bosses. But pacing will be important.

I recommend playing some top games from previous years to get a better idea.

The short answer is it depends, but also yes it is important.