I'm not a big proponent of applying tool offsets in part setup's 'Z' parameter but that's only because we use to do most of our work off of a tooling plate, leaving that surface as the common datum. That, and I remember a few crashes due to offsets that weren't cleared out before a program was saved... and/or were simply missed by the operator.
On parts that are somewhat flat, or perhaps where you're only drilling and interpolating thru holes/bores... you could always opt to set the tool off the top of the part with .0015-.002 with shim stock, set tool zero and be done with it. Eliminates the need to offset and reduces the chance for data entry error.
The Manufacturing Reliquary
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