Who's to say you had to raise the input trim though ?
Know I get of course that you find it sounds subjectively better increased, but that is simply your opinion of things.
What if I plugged my guitars in and found that maybe I felt the input trim needed to be cut a little bit, and what if I even had weaker output pups than you did ?
Things like input trim, preamp gain, master volume et al, do not have a "correct" setting, they simply having settings, and should to tweaked to taste. If things like MV, input trim etc were NOT meant to be adjusted, they wouldn't be a knob, but instead fixed variables.
Why bother making something range 0-10 if its only 'supposed' to be left at "4" and never touched, right ?
In short, you didn't have to raise the input trim, there is nothing wrong with your guitar or your pups, you simply like it better with it increased. I'm usually the opposite, cutting it back with most of my HB guitars, because my taste tend to be a little more towards edge of breakup and classic 70's tones.