Going between dungeons to get the shinies is a valid tactic! It can make the bosses easier, especially if you get some of the extra HP boosts.
The current rough plan is for this to stay short so we can get something out, with this being intended for the co-op bundle. Then we will look at either starting on a larger game in this style with an overworld and more story. We may also first look at restarting and finishing Recharge Your Rocket. We were still very early in learning Godot with that one, so had to cut a lot for the jam. In the current version you mostly only play in the overworld, with a bit of the initial building having been added. We had planned for you to enter the buildings at each energy site as well, with them being short dungeons. With our current skills it should not take too long to rebuild the game in Godot 4 and finish the additional content we wanted for it.
Glad you are enjoying the game! It is still early, but we are happy with how it is shaping up.