The ship designer's current behaviour is effing stupid, but I've come to expect nothing less from the Stellaris devs.
How is defaulting to upgrades stupid?
It's not displaying the wrong components. See, the system is designed to make life easier for the usual case. Every time you click any design, it'll automatically select the most up to date piece of equipment for any slots on the right. So when you select the design, you aren't seeing the actual design - you're seeing the design after the computer tries to help you.
that said, having a higher reactor does give some benefits, albeit maybe not worth the cost (depends on the person, I guess).
additional power on a ship gives increased stats (like speed, damage). So it is not entirely useless, but it depends on wether you want as cheap ships as possible, or ships that you squeeze as much juice out of as possible.