I have a Segger jlink (edu), which works great for debugging.
It can also program in the JFlashLite app (one of Segger's utils), but I haven't taken the time yet to figure out how to use it for this specific chip.
I put in an issue for this, expecting that this is not suppose to be supported. Its something I have to figure out anyway, so if I find a solution I plan on sharing it with the community.
I think in Segger's device the license is managed on the hardware itself, because I get errors when trying access non-edu utilities, which their site is a little misleading in which can and can't be used... but the app will tell you when you are wrong lol.
I also have a ST-Link, which the IDE lists as a programmer that can be used. But I haven't tinkered with it yet.
Seems like a weird decision to choose a chip for open software to only be pay-walled by the hardware groups. But, such is the way of the world I suppose.
Some boards come with their own debuggers, or built in tools, ESP32 and STM comes to mind. They almost seem more inviting by giving you tools up front, rather than having to pay for more stuff that you should have as a developer for that platform anyway. Definitely seems like a wiser choice for hobbyist like myself lol.
Had there been a disclaimer that the Uno R4 did not support programming in the IDE, I would have probably steered clear of it.