OK to be clear, if the dist rotor is pointing at #1 terminal, the pickup/sensor was passed 28* prior?

The sensor is attached to the dist housing and the cap is also. I'm assuming both are "keyed" to the housing in order to maintain their positions. The fact that the rotor spins iin relation to those points is irrelevant. It has to spin.
This is distributor phasing.
There are several ways to change the phasing, as mentioned before we can realign the rotor to the shaft, we can realign the shutter to the shaft, we can realign the cap to the housing or we can realign the sensor to the housing.
What I'm trying to get to though is if this is whats needed.
So how is this 28* number determined? Is it something the ms system measures during setup? Is it something you program in?
Without separate cam and crank sensors this is not something ms can measure itself.

Also, think about this, you have 8 flags on the shutter wheel, one for each cylinder and they should be an equal 45* apart. The same can be said for the cap terminals. Basically you can make any terminal #1 and any flag #1 but they should still give you the same 28* reading unless something is machined wrong.

This leads me to question the statement that this 28* is a measure of the spacing between the pickup and terminal. Is it actually the measure of the difference between TDC and the pickup? That makes ore sense.
To answer your last question, it depends on what this 28* is measuring. If it measures the space between pickup and rotor, then relocking the drive gear has no effect. If it measures the degree change between crank and sensor, then yes it may help.

In either case the phasing of the rotor to terminal will need to be checked and adjusted. But we need to get the first problem fixed. Rephasing the rotor is easy.