I just spotted your post. It's just over one year since you posted it. No one replied.
I'm having a similar problem and would like to debug my customizer as well.
I can load the C# customizer code into Visual Studio and I can modify the user interface and see the changes in Creator.
The problem is that if I code part of the customizer incorrectly, I can't reliably debug it from Creator (your question) and I can't debug it from Visual Studio.
Hopefully Cypress development will take note of this post again. Maybe they can share a way to install the UserControl code of the customizer into a Visual Studio form so that we can debug potential issues within Visual Studio first.
I haven't worked on the custom customizer since then (life happened), but i do hope Cypress can help us to work with their tools.