Okay, here goes...

Master mode is not like the other Modes.
It only references programs stored in the other principal modes.
For example, a Master might "reference" a VOICE, or a PERFORMANCE, or a SONG, or a PATTERN.

This means if you overwrite the Master that is referencing a Voice, you do not destroy the Voice.

So think of the 128 Master locations as you own personal "Performing Set"

Let's say your first Set on stage requires the following setups:
An acoustic piano, followed by an electric piano, followed by an organ layered with choir, then strings, an acoustic piano, then finally piano layered with a pad.

You could try jumping back and forth between VOICE MODE and PERFORMANCE MODE attempting to recall these setups, or you could use the Master mode's first six programs to easily organize/recall exactly what you need at the touch of a button.

Master 001 could reference "Full Concert Grand" piano
Master 002 could reference "Vintage'74" e.piano
Master 003 could reference your own custom Performance layering B3 with a choir
Master 004 could reference "Medium Large Section" strings
Master 005 could reference "Full Concert Grand" piano
Master 006 could reference your own custom Performance layering a piano with a pad

The Master only "points to" a location in one of the other Modes. This allows you to place your favorite things to play into one BANK of 128 Programs... Now you can even use a Foot Switch (set to PC INC) yo advance through your setups.

Overwriting Master setups can be done quickly as necessary..

The ones that come from the factory (Factory Set) are there to learn from. As you advance from Master 001 through Master 008, for example, you will see that not only is the Master mode L.E.D. lit, but so is one of the other four principal modes. And in the screen you will see that the program it is referencing ("pointing to") is identified.

From the main Master screen:
Press [F2] MEMORY
This is where you can point the current Master to any of the principal MODES and a specific MEMORY location in that Mode.
Notice that pressing [F6] will allow you to GET NAME... this automatically copies the name of the referenced Memory location to this Master program.

When you press [STORE] the name of the referenced program, be it a Preset or User Voice, a Performance, or one of your Songs or Patterns!

As to writing into a blank space, well that is not how it defaults. The 128 locations are filed with "placeholder" data.
If it really bothers you having other data there... You can initialize a Master location, as follows:
Press [MASTER] to enter Master mode
Press [JOB]
Press [F1] INIT
You can select "ALL" and press [ENTER]
Press [STORE]
You can then store this into the rest of the locations... One-by-one.

An alternative is working with the John Melas third party editor suite, which lets you assemble Master mode setting on your computer.

Hope that helps.

Thank you Bad Mister, for explaining in detail. Now I know how to utilise MOxf better.
😉