We've released version 5.7, this has a lot of fixes for Rider. It's still in the review process for acceptance to the market place. In the mean time the manual zip install for Rider can get you access to it a bit faster.
The release notes are here:
https://www.ncrunch.net/...owChangeLog?version=5.7
The download is located here:
https://www.ncrunch.net/download
I've improved the toolwindows specifically for the issues you reported. However, the menu was always accessible for me. The Windowed mode and the Options Dot are fixed. So I hope that the menu is fixed as well, if it isn't please let me know.
Thanks again for taking the time to report the issues.