We developed a product using the RP2040 and had to use Thonny. PhCharm wasn't handling the upload/run/debug process well. If I remember correctly, it had to do with the mechanics of the console. We developed in PyCharm and simply used Thonny as a code uploader/debugger. This worked well. Not sure it would be a good fit for complex projects. Of course, that isn't the intended use case. It's a nice IDE and a commendable effort.