Query Designer is a bug and should be removed/commented out

Currently as far as I know Query Desinger in Report Builder is built-in and by design.

See: Build a Query in the Relational Query Designer (Report Builder and SSRS) 

'QD holds separate hidden querys and parameters, ie dataset properties and QD can get out of synch'

About QD can get out of synch, you can consider sharing more details about it like a sample.

In addition, you can create a new idea here for Query Desinger to help us improve Power BI.

It is a place for customers provide feedback about Microsoft Office products . What’s more, if a feedback is high voted there by other customers, it will be promising that Microsoft Product Team will take it into consideration when designing the next version in the future.

Best Regards,
Community Support Team _ Yingjie Li