To an extent that's true of course. Of ANY product.
Obviously any brand of boat with a Yamaha outboard has that engine built by Yamaha. Any boat that has a certain brand of ANYTHING is going to have that in common.
Getting down to the component level, I would not be surprised to discover that things like decking material, carpet, wiring, aluminum stock (tube & sheet) and assorted hardware come from common vendors for at least some items.
That said, you can go to Home Depot and in the same aisle of the same store buy grade 5 zinc plated bolts and grade 8 stainless steel bolts.
In other words, it's not who you buy FROM, it's WHAT you buy from them. Two vendors buying aluminum flat stock to build their pontoons can buy different thicknesses and grades of aluminum. Two vendors buying carpet from the same manufacturer can specify different products.
So on and so forth...
Boat building, and this goes for fiberglass monohulls, pontoon boats and steel yachts, is still very much a custom shop business.
If you want to know the specifics for the Bennington manufacturing process, I'm sure they'd be happy to tell you all about it. Bennington is a high end product and they REALLY like to brag. In fact, don't get them started if you don't have the time.
All that said, the simple answer to your question is that while there are manufacturers out there who buy "generic" parts and slap together inexpensive products, any of the high end manufacturers (Bennington, South Bay, etc) are making what is really a highly customized product.