With indexed stock - Cut depth is limited to A axis (Z over right, Z Bottom and model Z offset not recognized)

[Vfr750rouge]

When Stock is indexed, the cutting depth is limited to A axis limit in depth, Z over right, Z Bottom and model Z offset are not taken to consideration to remove material after A axis is reach during roughing.
Z thru allows cut passing A axis but surface features are not recognized and cut away - only usable to for drilling.