Hi @mateuszploszajmazure! This is not directly a response about the issues in RIR but mostly a response to your original question about possible workflows to prepare the mode.
We are developing a Revit plugin (Pollination Revit Plugin-Coming Soon) to exactly streamline processes like this one. I test your sample model and it works with no issues. It does simplify the windows and removes the double panes, etc.
Here are the hbjson and 3dm files.
Do you mind sharing the more complicated model that you are struggling to export for testing?
example_model.3dm (1.5 MB)
example_model.zip (19.3 KB)