Hi Ulf,
I'm also having problems using the Make Query Table tool in Pro's Model Builder. I did not import this model from Arc, but am building it from scratch.
Basically, I want to be able to make the query a parameter of the tool, so users can select a certain date subset of data to use. The tool will run fine the first time in Model Builder, but after saving I can no longer change the expression using a parameter variable. I get the the "can't be edited in Clause mode" warning you mentioned, as well as an error about the expression not being able to be initialized. It looks like this is because the Clause is populated be the input data set choices, and the Model doesn't have access to this information until the process starts running, so there is no way to construct the parameter beforehand. I'm researching it further and trying different methods.
Frustratingly, the only reason I'm using this tool is because the Add Join tool does not honor the layer properties definition query on tables the way it did in ArcMap, so I have to use Make Query Table first. I currently have a case with ESRI Support to get this other bug documented (and maybe fixed?).
I'll let you know what I find, but wanted to 'bump' this thread in case others are also struggling with this tool.
