Could this be run alongside a barbell program like 531?
Should you? Probably not. Could you? Sure - but it as others have implied, it wouldn't really be in the spirit or the intent of the program.
IMO, a key factor is what you are attempting to use each program for. Which will be the supplement to the other, or will the intent to be improvement in both concurrently? This is important because you will need to back off one or the other at some point. If 531 is impeding your ability to recover enough to get through your Giant work, you may need to adjust the 531 program, or vice versa, depending on
your intent.
Both camps will likely say that you aren't doing their program correctly (as programs are designed with a specific intent), but you are obviously free to experiment and use them as frameworks for your own training programming.
I'll also add that contrary to the initial offering, there are now tons of 531 options in Wendler's later books that focus on the assistance more than the barbell work, where the barbell essentially provides the strength foundation, and the assistance programming focuses on improving conditioning, work capacity, hypertrophy, etc.
You could use the frameworks of the Giant to add conditioning and work capacity training to your 531 program, but your experience would be your own and any issues, challenges, or benefits couldn't necessarily be attributed to the Giant program.