Other bird figures from Flint Ridge are seen where the artist exploited natural crystal formations as 'eye' features on the birds. It may be this artist had a nice bird figure but without a more desired 'crystal eye.' So a synthetic eye was made by the clear varnish material mixed with some quartz crystal pieces from elsewhere.
Careful examination of art pieces like this can provide information about the material culture of the people who made them. X-ray florescence (XRF) testing might be able to detect the chemical composition of the clear varnish substance.