So I have both just trying to clarify here.

Previously used master vessel binding to copy spirits to a necklace. Long story short -> necklace broke.

So I bought a transmute bag to move them all back to their original vessel.

Looking at the options the transmute bag has, can't I use the bag in the future to copy the multiple spirits to a new vessel? If so what is the difference between the master vessel and transmute bag?

To me, they seem the same except the transmute bag has more than one purpose. Or maybe I'm overthinking this.

If you used the copy function of the master vessel, the original bindings are still in the original vessels. You don't need to move them back to the original vessel.

The transmute bag cannot make master vessel. Master vessel is a vessel that can carry numerous bindings without the risk of clash of energy when the bindings are not compatible with each other. E.g. some DA spirits may not like to be bound in the same vessel with WA, and vice versa. What the transmute bag can do is make a vessel with multiple bindings, but no guarantee if those bindings would be compatible with each other or not.

: )