Questions about cloning

[sudodus]

That is how it works. But if one drive is made for UEFI mode and the other one for BIOS mode, you must also switch boot mode in the UEFI/BIOS system. Many computers (but not all) can be set to select automatically whatever boot mode is available (the bootloading structure found in the drive(s) connected).

I think you can go for a Xubuntu-only system. If you change your mind, it is easy to insert the Windows drive too (and test which is the best way to arrange the drives, if/when necessary).

In principle, Linux does not care much about the drives except for booting, after that it cares about the partitions and the file systems in those partitions. The partitions can be anywhere, in one single drive, in two or more drives, even in an external drive, for example a USB drive. If configured for it, an installed Xubuntu system is even portable between computers (use the internal Linux drivers, avoid proprietary drivers for graphics and wifi).

[C.S.Cameron]

Why not install Ubuntu to an external SSD. That will be fast enough and should not mess up your Windows drive.
It will work on both BIOS and UEFI computers.
You can take it with you when you travel for use on other computers if you wish.
You can test the method with a 8GB or larger flash drive and a persistent install of Ubuntu using mkusb.