The Onan is right under the dinette in our Itasca, but the floor is thickly carpeted. Our Onan is not that loud ... we can sit at the dinette and eat with the Onan below us running w/o being driven out. I also use a special spark plug in it, which has smoothed out it's sound so it sounds "less labored" (hard to explain), and thus quieter.
Before getting rid of your built-in generator, you should consider lining it's compartment walls with good marine-grade fireproof sound proofing material like what is used in boats to help absorb main engine and generator noise in their compartments. Maybe also throw a rug on the ground under your RV's generator to absorb some of it's downward exiting sound so it doesn't bounce straight back up towards the floor of the RV so much. There's even higher quality vibration isolation mounts for generators that could be retrofitted into your generator's mounting frame to help reduce vibration in the RV's structure when the generator is running.
I consider the convenience of a remotely started built-in RV generator fueled from the main tank to be just about priceless. I'd certainly try everything in the book to quiet it down before eliminating it. Your built-in generator may be the most expensive single item in your coach ... it should be made to be as usable and tolerable as possible.
For what it's worth - we once ran our Class C's Onan nearly all night when drycamping in extreme heat and humidity conditions that we had no choice but to somehow endure. We were both able to get a good night's sleep. That experience made a believer out of me.