It doesn't matter where you place the spindle prior to zeroing the B axis, as long as the point lines up with the center of the rotational axis of your indexer. I have a chunk of 2x4 that I stand next to the work on the indexer mount that lines up with the center. To zero, I back off the X axis by 2", zero the B, then move back to the "zero" position. My indexer is oriented on the X axis and the gantry moves the Y car only.
If you examine an indexer machine code file, the axis your indexer is oriented on doesn't even have a number. It's blank. As I am on the X axis with the indexer, all X axis values are missing from the machine code. That means that it is irrelevant what value the X axis reads on your machine when you are doing indexer work. I zero the Y axis about 2" away from the chuck. It is very important NOT to run your end mill into the chuck. It can be a costly and embarrassing error. Don't ask me why I say this.
ShopBot Details:
2013 PRS 96x60x12 (Centroid upgrade)
4hp Spindle
12" indexer
Aspire
Rhino
Fusion 360
Ferrari 360
Prusa MK3S+