The benefit of the HF trailer is that it is reasonably priced, can be shipped, and anyone can have one. They aren't the optimal design, but they will easily work.
The custom trailer will be exactly what you specify. If you know what you need, thats what you'll get. (within reason) If you want a low riding trailer, the custom built one can be just as low as the HF ones. Use the same tires. You don't have to have the taller tires that most people put on their trailers. The custom builder can actually duplicate the HF trailer, as silly as that seems. You can get an 8" tire/wheel that will handle 1,165lbs each.
http://www.etrailer.com/Tires-and-Wheel ... 3H325.html
Even the standard, find it everywhere, 5.70-8 load C tires will take 910lbs per tire. Thats 1,820lbs for trailer and stuff. If you don't mind carrying two spares, the load D tires carry 1,075lbs. (D tires aren't readily available everywhere) I switched to 5.30-12 C tires on my 2,000lb trailer. I wanted the extra 2" of height, and I can find them everywhere when we go on trips with it.
Another reason for the custom trailer is you can get the higher capacity axle, and spec a lighter/longer shock. Durable, but still get a good ride. $300 to get exactly what you want seems to be a good deal to me.
Michael