So, they discarded the form of the face coming from iconography BUT used the colors like hair and skin. This is SO catholic (well, or religious in general).
You imply that there is only one "form" of his face depicted in iconography, but this is not the case. There is wide variation in how he has been depicted going back to the 14th century. Here is a selection of images from the 14th and 15th centuries which are closer to the reconstruction than they are different:
https://upload.wikimedia.org/wikipedia/commons/c/c2/Lippo_Me...
https://www.kressfoundation.org/kress-collection/artwork/498...
https://catholiceducation.org/en/culture/art/saint-thomas-aq...
https://catholicclassicalict.wordpress.com/wp-content/upload...
https://www.wikiart.org/en/fra-angelico/st-thomas-aquinas-14...