Coolfox,
Some encoders have a separate 'index pulse' in addition to the regular incremental quadrature. My encoder has this, but the motor is geared down to the spindle, so I can't use it for indexing and therefor I added a separate photointerruptor to the degree wheel.
It is not neccessary to zero the machine after homing unless you are recutting a part that has already had indexed operations done to it, or if you want to use absolute azimuth locations. Another reason would be to have the DRO numbers be meaningful for monotoring purposes. The Mach manual describes the A axis as 'infinate', and I have taken it to the tens of millions, so I don't see a practical limit there, and if your Gcode utilizes only relative (incremental) moves, and a DRO showing rediculously huge numbers is not a problem, then you would not need to zero the A axis.
Fixture offset is unaffected by the A axis shenanigans . . so far anyway.
My objective is to make a sort of 'mini machining center' and emulate as many of those funcitions as time and budget (and Mach3) allow. A combined spindle/indexer is, I think, the first and most important step, and I have that pretty much worked out. I've just been prototyping to test feasibility up to this point, but I'm satisfied now that the concept is proven out sufficiently to start designing a sturdy permanent head with reasonable quality ball bearings and alignment pins and table mounting. I'm going to have two gear ratios 3:1 and 2:1 to accomodate different materials and stock diameters.
EDIT: checked out your site. That is some seriously unique and beautiful jewelry! I pray my wife never discovers your site . . .