I checked the StrataGem manual and it pointed to these two references describing the theory:
J.L. POUCHOU, F. PICHOIR and D. BOIVIN, Proc. ICEM 12, Seattle 1990; Microbeam Analysis, San Francisco Press, (1990), 120; ONERA Report TP 1990-109.
J.L. POUCHOU and F. PICHOIR, Electron Probe Quantitation, ed. Heinrich and Newbury, Plenum Press, New York, (1991), 31.
I also have this reference which shows an early release of the software with examples:
J. L. Pouchou, "X-ray Microanalysis of stratified specimens", Analytica Chemica Acta, 283, 81-97 (1993).
If I were to cite one, it would be the 1993 article.
Best regards,
John Minter