What is the best way to achieve this?
Use either an Ubuntu or Debian-Live based derivative if you want to create a persistent drive using Rufus.
The problem is that Linux distro maintainers can't agree to a common method of enabling persistence (heck, they can't even agree if the kernel parameter to provide should be called
persistent) and every other distro seems to be falling prey to the NIH syndrome where, instead of looking at what others do and trying to follow suit, they appear to be reinventing the wheel...
Then end result is that it makes it extraordinarily difficult and time consuming for an application like Rufus to try to detect and support every method of enabling persistence out there. As a result, Rufus only supports the method of enabling persistence for the two most common methods used by Debian or Ubuntu.
Most likely, ArchCraft does not use either of a Debian-like or Ubuntu-like way of enabling persistence, and whereas Rufus will have created a persistent partition that is compatible with Debian (default), ArchCraft is unable to use it.
Thus, if you want to have persistence working with a drive that was created by Rufus, you need to use either Debian-Live (or a direct derivative of Debian-Live), or Ubuntu (or a direct derivative of Ubuntu).