Got the go head from IMC folks and SEI.  Locked up the HAM3 HEPI.
The largest displacement see from unlocked to locked condition is 300 cts or 0.0005".  The runout of the vertical shift is only 140cts so max tilting of the table is only a couple urads.  I see a similar change in the yaw position.  In conclusion, alignment should be very little affected.