Chilis have a natural variation in heat, which depends a lot on growing conditions. Jalapeños can range from ~2000 to 8000 scovilles. The hotter ones don’t taste different, they just have more capsaicin. That molecule itself has no flavor, it just triggers the heat receptors in your cells.

Maybe your perception of the heat has gotten entangled with the flavor so cognitively one is less satisfying without the other. But that’s specific to your perception and not how it works at the chemical level of the plant or human sensory cells.