This problem only impacts gui when it is embedded in the project page. This does not happen on the standalone beta build.
If you open the note picker or angle picker, then open the extensions library (for example) you still see the field above the modal.
It seems that this code to hide the block editors is not running when opening modals when the GUI is embedded in WWW https://github.com/LLK/scratch-gui/blob/develop/src/containers/blocks.jsx#L133-L135
My best guess is that the state tree may be different and the anyModalVisible prop may not be setting correctly in mapStateToProps https://github.com/LLK/scratch-gui/blob/develop/src/containers/blocks.jsx#L558-L561
Thanks to @picklesrus for finding this