While installing 2 operating systems, 1 each on a separate partition might seem like it would enhance security in the same way as physical isolation (which requires two separate computers). Dual booting is not recommended.
The following could apply to any dual-boot configuration. Such as a Windows and Debian dual-boot configuration.
One problem is that when you dual or multiboot, even if you are using encryption on your Qubes installation, /boot is still unprotected and could be maliciously modified by the other OS, possibly leading to Qubes itself being maliciously modified.
The other problem is firmware security - for example the other system could infect BIOS firmware, which might enable compromise or spying on the Qubes system.
If the bios firmware was infected with malware an encrypted bootloader would not be of much help.
Best case would be to use the computer for Whonix use only. But thats’ not always an option for everyone such as in this case. Running Windows and Whonix in VirtualBox would isolate the VMs from each other and the host. That alone would be reason to use a hypervisor over dual-booting imo. You would want not want to use the host (debian) for any online activities. You would only update the packages on the host and nothing else.
You should also check out the Whonix wiki for more on securing your host and Whonix. These are just two of the many chapters dedicated to this subject.