I read a post once, or a video - I cant remember - But the general idea is - For standardization and good practice - Is to keep Home 0. Always. Doesn't matter if it is x,y,z. And the regarding the z Axis, I also tried it once to have the Bed zero - The problem is, the bed changes over time as you work. This is not a good setup. The Top does not where you put the home sensor. I do think it is better just to keep Machine Coordinates G53 -ZHome 0 (Top) and work down from There into, - values. This makes sense when working simply because - when you probe the material - for me that is - the top - When I see a Z -5 I know how deep I cut into the material. Basically, It will not matter either way on your workflow, because you dont use G53 when you cut stuff - You work in G54 which is 0,0,0 to your workpiece.
Then regarding the master tool - I'm open for input but I dont see the need, as this is an extra step for me that adds no value. Because I can use any tool, which length is known, and offset applied to probe the Z. I assume this will work the same in 5 axis, if you need to probe the side of material. I dont know if it works that way.