I have patched the control issue and am waiting for the jam to end to drop the update, which will also fix some other issues so stay tuned :)
The game uses the theme in 2 ways: Exchanging score for points in the Shop (open via pause menu) and exchanging firing weapons, boosting, and shielding for heat production. If you count the weapon types with different stats then that's 3 ways. But yeah, it's not really much of a "boss rush" specifically...