That video I included may help you gain a clearer picture of what all this stuff is about.
The stuff shop said about the axle being "downrated" is the reduced rubber so that part is good. He is saying heavier metal axle tube with less rubber inside to provide a softer suspension. Softer suspension = less slamming from road bumps.
Do not run your tires at 28 psi, soft tires run hotter than firm tires, heat degrades tires literally from the inside out. Can have good tread and tire just fails.
You should be closer to max than min air pressure especially if doing 55 - 60 mph for several hours traveling. A little under max is not a big issue but 28 psi tire pressure is part of the reason those Ford Explores would have a "comfortable" ride right up to when a tire blew and the vehicle rolled over because it sat high. Dealer told people to go with a lower pressure for a better ride. Trailer tires have a weight
rating based on the tire pressure, reduce the pressure and you reduce the weight
rating. Talk to a tire store to get better information.
Your trailer is going to sit higher than it did originally, how much depends on the down angle of the axle. Tire is mounted to an arm, the arm comes off of the axle tube that runs across the trailer. That arm can be level (0 down angle) or angled up by between 10 and 45 degrees (up angle) or angled down (down angle) by the same range of 10 - 45 degrees. Worth asking what angle the torsion arm was ordered at. I don't recall exactly so maybe someone will chime in who does but I think 5 degrees equaled about a half inch of height. So he may have ordered axle at a different angle than the original to compensate for some of that additional height from the bracket.
Here is a post that has a picture of the axle (you can see the arm angles down relative to the bracket by about 10 degrees)
Scamp Axle - Leading vs Trailing
This Dexter Axle video is even better but when they show the axle and tire moving at about 1 minute into the video you can see the arm is above the bracket (10 degree up angle)
Dexter Torflex® Suspension Axles - YouTube
If it makes you feel better a lot of people do increase the height when they replace the axle in order to be able to handle some rougher back country roads. You might need to get a little step to put outside your door to step up an extra 6 or 8 inches.
I do not know the particulars of your trailer but I do recall a long thread on replacing an axle (with pictures) where yes they cut the frame and then added some reinforcement to compensate. However that person was doing the work with a friend, if the frame broke it was all his own fault, a shop might well be reluctant to take that chance with a customers trailer. Paying a shop for that sort of custom work would add to the cost.
Hopefully they at least ordered the axle with the plate that allows one to add brakes later if desired. Those plates are not expensive when ordered as part of the axle, cost more to add later. If he did not order with brake plates it would be worth asking him to contact Dexter and see if the order can be modified, depending on the additional cost and your willingness to pay it. Ordered does not equal built, Dexter builds axles to order so there may be time to get this option added.
I am not impressed with the person you are dealing with at this shop. It can be a bit of a challenge to provide good advice and information so that a novice customer is making an informed decision. But hey that is part of the job, I did not go to med school so I expect my doctor to explain the condition and options so I can make an informed decision. People do that same explaining and advising on options for repairs or modifications to FGRV's all the time here on the forum.
Bottom line don't panic, but do not take this shop managers word as gospel either. And yes a lot of the experienced members will be annoyed at this person on your behalf and will tell you why but in the end I think even if not the optimal solution experienced person would have gone for it will probably be satisfactory.... as long as you don't run 50 psi tires at that stupidly low air pressure!