Welcome @columbine84, to the community!
this reason is actually also stated in the AN5571 you referenced:
[page 2] The reference junction is at the reference temperature and, in order to ensure a good stability, this reference junction is generally measured by a thermistor.
...
[page 3] The output of the thermopile can vary depending on the ambient temperature. A thermistor is generally used to compensate this possible drift.
Hope that answers your question?
Regards
/Peter
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