I think I figured out the problem. SEO Page Generator is filtering out the <script> tag that wraps the JSON-LD data.

Just FYI, we are working on updating our Schema.org markup to JSON-LD, so keep an eye out in future releases

@Steve Goldberg, this is excellent news. The problem for us is Google Merchant Center. Google Merchant Center only recognizes product variants for clothing and not other types of products. I am working a boat parts website that has lots of matrix items, and each sub matrix item needs to be defined in it’s own schema.org product type. These product types need to be repeated on the PDP for each sub matrix item. In a single word … Yuck. I had plan to remove the Schema.org microdata tagging and replace it with the more concise JSON-LD. Because the <script> tag is being filtered out, I have to do it with the microdata. 😞