Both VMWare player and QEMU support booting from "Physical Drives", which basically is nothing more that booting from a disk that is already present in the host.
When you are using QEMU with QEMU Manager the option can be found on the Drives tab:

The booting device of the host is typically PhysicalDrive0. Your USB devices should be PhysicalDrive1 or higher. Make sure you select the right one.
In VMWare the option is not directly available when creating a new VM. First you have to create a virtual hd of any size and finish the VM. After that edit the properties and delete the created HD. Now add a new hard disk and select the option "use a physical disk (for advanced users)":

Just as in QEMU the booting device of the host is typically PhysicalDrive0. Your USB devices should be PhysicalDrive1 or higher. Make sure you select the right one.

There is also a selection for using the whole drive or individual partitions, but for USB flashdrives you can leave this on "use entire disk" (as partitions on USB flashdrives are hardly supported and unusual).
A screenshot of a proof-of-concept running the miniXP from Hiren's BootCD in VMWare player. In this case the USB flashdrive was formatted as FAT32, but for me it also worked when it was formatted as NTFS. I used grub4dos as the bootloader/manager.

and the properties of the virtual machine in VMWare Player:

Update: to prevent the VM from hijacking the USB flashdrive remove the "USB controller" from the VM properties.
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