By using pressure altitude.
Therefore the performance ceiling is calculated in a standard atmosphere, and presented in the same to the pilot. Obviously the geometric performance altitude can vary quite a bit.
Similarly, the certified ceiling is presented in pressure altitude, and the testing is done relative to pressure altitude. So again, it's all in the same units.
Your question is similar to asking how oem's allow for the variation in true airspeed with indicated, according to atmospheric factors. With a few exceptions, we don't. We use IAS consistently in presenting info, limitations, etc. All the IAS/CAS/EAS/TAS happens out of sight. Same for pressure/geometric/geopotential altitudes.