While Sea~Doo boats and jet ski's share the same engines and drivelines in some instances that's where they part company when it comes to setting up the carbs and tuning them properly. Consider what the factory originally published for carburetor tuning specs when the boat was new, those specifications were happy mediums for brand new hulls, peak compression engines etc.
Fast forward 15-20 years, boat hulls don't age well and they often gain considerable *dry weight* just from moisture making it's way into the glass lamination. Replacement engines built with aftermarket parts, while done well in most instances will not produce the same compression as a factory motor and you will lose some of intended manifold pressure and air volume the original engines produced that are the driving force in operation of the carbs.
Add in the ability to load the hull with four passengers and their gear for a day out on the water and there's realistically close to thousand pounds of added load, you have to work at it to get boat carbs tuned properly.
For new engines, a complete cleaning and rebuild would be in your best interest for performance and longevity of the new engines. It's important to final tune the carbs with the boat in the water, under a load to ensure they are set up correctly.
If your local service provider is doing all of that for the price you mentioned, that is more than fair for that service. If all they are doing is twisting the high and low circuit adjustments on a trailer while the engine is running on a water hose look elsewhere for help.
