I think I may have figured it out. Time will tell.
I was really tired yesterday after loosing several hours of work to a smoothstepper screwup that turned into a huge gouge in my semi-finshed sample sheet for a local cabinet shop. Since the A (slave) motor has no actual limit switch it seems normal that tripping the home switch defined for A would not generate an eStop. That's why the A "prime" sensor remains lit without an eStop. The problem seems to be that I got lost in all the settings and tried so many different combinations of code I failed to notice that when the refcombination(10) executes it does indeed back off the A side prime sensor. But when the Y squares later it pulls the gantry sideways and re-trips the A prime sensor because the switches are adjusted incorrectly. If I defined the prime sensor as a limit switch for A it would probably generate an eStop if the M4 prime sensor were tripped, which is probably what I want. I'll try it when I get a chance.
I went down there this morning with fresh eyes and carefully watched it and went thought my configuration again and discovered I had the Homing/Limit setting for the A axis set to reverse the DRO which, of course reverses the homing direction as well. My motors are defined different than the stock 22 tooth XML from cncrouterparts. I swapped X and Y and had to fiddle with A motor directions to get it working correctly. The A motor has to be reversed in relation to the Y motor since it's on the other side of the machine. That got me thinking I had to reverse the DRO in Homing/Limits which homes away from the switch rather than towards it. That's why I got upset and just enabled "Home Slave with Master Axis" and just used the Y sensor. The issue is also that its difficult to square the gantry without moving the tool around and measuring it. I finally measured tool to frame distance across the X axis and found that the sensors were indeed setting Y axis square with the X. So, I think it's OK. I'm re-running the same job this morning and so far, other than the smoothstepper giving me an error every once in a while, its working OK.
Thanks for the replies.