The short answer: Because they can. It's Frontier's game, and they can do whatever they like with it. We're here to play. If it bothers you THAT much, you'll want to be sure to purchase enough Frontier stock, assuming they're publicly traded, to buy your way onto the board. Then what you want will actually matter.
The Long Answer: Because the new Grade 5 upgrades are part of the new Engineering system. Had the system not been changed, you could think of these new Grade 5 modifications as being "Grade 6" instead. But Frontier didn't want to add a new Grade 6 along with the new engineering system, so instead, they truncated the values of the old grading system, and the top-end, I-spent-1000-hours-min-max-rerolling-to-get-these-results results are only good enough to be the top end of the new Grade 4.
You didn't lose anything, your e-peen didn't shrink. Instead it gained more room to grow.