All 'running in' brushed motors achieves is getting the new square ended brushes to conform to the shape of the commutator. Doing it the water way just softens the brushes, keeps it cool and floats the worn bits away, depositing a lot of it all over your motor, it also washes away any lube in the bearings etc...
it was a method used by stock RC car racers where you were given an out of the box 540 motor as part of your entrance fee so no one had an advantage, some people would connect it to a battery pack, drop it in water for a couple of minutes, dry with an airline and install in car and race it -the idea being that the brushes being worn to the comm' shape would allow more current to pass and result in a quicker motor.
If you want to bed your brushes in, connect to a single cell, or two and leave to run slowly until the cell goes flat, blow out the crud and install in your model, similar result.