SSIS project parameters do not work the same way as SSIS packages. All project parameters are stored as XML elements in a single XML document for the entire project called Project.params. This is the core reason why packages have a good overwrite story while parameters have a poor overwrite story.
It should be obvious that BimlExpress can’t just overwrite your Project.params file. Of course, BimlExpress would be creating the parameters you specified in your BimlScripts, but it would also be overwriting any parameters you might have created manually. If you are a Biml purist, you might not care about this, because you would be fine with creating all of your project parameters through Biml. Unfortunately, most Biml users are not Biml purists – and even fewer development teams are Biml purists.
It’s a bit of a tricky situation for those cases in which you do want a pure Biml solution, and I’m glad Catherine got down to the bottom of it.