When booting gateway or workstation if I open the settings of the guest OS that is booting, this message shows up by virtual box “The machine settings were changed while you were editing them. You currently have unsaved setting changes…” whereas I haven’t changed anything. I noticed this issue when opening settings immediately after starting gateway (or workstation). Along with this message, sometimes even the screen of the guest OS gets black and freezes! I wonder what exactly opening the settings window has with what’s going on inside a guest OS!
Host is Linux.
This is a VBox problem and is better reported upstream. VBox is known to be buggy. You are better off using KVM since you are on Linux.
When you say this is a VBox problem do you mean this is a known problem? Have you ever encountered or heard about this?
By the way VBox is much more convenient to use than Qemu.
You don’t have to do everything via the command line. There is also virt-manager which is a GUI similar to VirtualBox.
When I say this I imply it is not the fault of Whonix. There is nothing a guest OS does that should cause the hypervisor to breakdown like it did.
I hope you mean KVM because plain QEMU is emulation and that is mighty slow. Also as @Algernon mentioned, the virt-manager GUI should be enough for your needs. The Whonix wiki should help you for any Whonix specific instructions.
PS. How is your research going? Do you have time these days?
I’ve worked with QEMU and KVM a lot. Both with and without GUI. We all have to confess Virtualbox is still more convenient and user friendly with more features.
Interesting you remember me from last year 
Currently I’m following a couple of research routes. If you have something in mind feel free to send me an email. Maybe it’s close to what I’m doing.
Sure let’s discuss this via email. Can you temporarily post (I will remove as soon as I see it) your address in an obfuscated way for spam resistance purposes?
Since you know C there are a couple of tasks we would appreciate your input on too.