I don't think you should be having this issue with a brand new "top tier" boat. I'd compare with some other new 235 owners and see where theirs end up.
Even on my 20 year old 330, the drains are a couple inches above the waterline - and good thing, too, because after 15-20 years, the hoses start to rot and you'd end up with water pouring into your bilge.
Now, maybe you had 800 lbs of guests on board, and it isn't a super critical problem, BUT.. I'd be unhappy. And as you noted your "cheaper" boat didn't have this issue.
From your photo, if your boat was kept in the water, you'd have barnacles growing INSIDE your hoses. I'd escalate this to your dealer and grady corporate and see what they have to say. Seems like a pretty big oversight for a brand new boat, unless you have a lot of extra weight in the boat you forgot to mention? Was your boat listing to starboard (like, did you have 200 lbs of ice on board?) in that photo?
It may be a characteristic of that particular hull, but that doesn't make it okay.
Compare to photos here, where even with the normal-size-adult captain, the thru hulls appear to be an inch or so higher - although I found a couple more where bottom paint was drawn right through the middle of the thru-hulls, like yours:
https://sportfishtrader.com/boat/2020-grady-white-23-235-freedom-dual-console-for-sale/