We calibrate across the full range of altitudes that we measure, but if the single point adjustment doesn't bring the altimeter in line with table one in FAR 43 appendix E as required, we'd need to take a look at it. Note that the altimeter tolerances are tight at sea level, but looser at altitude. We'd expect that in most cases, after doing the adjust so you're on at sea level, that everything else will fall into place.
Now, keep in mind that that test applies to the altimeter itself. The part that pertains to encoder states:
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(c) Automatic Pressure Altitude Reporting Equipment and ATC Transponder System Integration Test. ..... The difference between the automatic reporting output and the altitude displayed at the altimeter shall not exceed 125 feet.
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Now remember, our altimeter IS our encoding device. At 29.92 (pressure altitude, which is where the tests are done), they differ by 0 feet, all the time. The pressure altitude being measured by the EFIS is ALWAYS reported out the serial port.