I was on my phone, allow me to expound.
1: Your thermostat being stuck open will never in anyway on any motorcycle in any year in any way cause OVERHEATING!!. It will cause the bike to run and stay cooler longer than is optimal for proper temps to be reached by the cylinder head. As a result you will almost certainly have some reduced gas mileage, but, the R3 ECU is stupid and has no idea the thermostat is stuck open. To reemphasis, the thermostat is a separate issue from overheating.
2. If you have a bad head gasket, with no apparent problems, which it seems you no telltale indicators, get a coolant tester to check for exhaust gasses in the coolant. This will validate that it is or isn't the head gasket 100%. The test kit is $30 and you can very very easily do it at home, it's a laymans tool, and easy to do!!
3. A crack in the block will 100% show oil in water or water in oil. There is no path for exhaust to get through the block into the coolant... period. NOW, if you have a cracked cylinder liner, that's different. It's extremely unlikely you've a cracked cylinder liner, so unlikely, that you'd be the very first instance I've ever heard of on any modern motorcycle, let alone a Rocket, with it's overbuilt everything.
Your dealer is taking you for a ride so he can charge you $2,000 in labor to disassemble the motor, a few grand in parts he will deem as "out of tolerance" but will have nothing to do with overheating. Then he'll put it all together, and in the thousands of dollars of pars he'll replace, inevitably one of them will have been the source of the problem, so it'll seem like it was "money well spent" because the problem is gone, when in reality, he used a shotgun repair strategy when a precise application of thought could have avoided all of it.
Your dealer is garbage, sorry.