The only publisher that told us flat out no was Green Ronin. Others have either given us Full Permission or OGL + Title only.
http://pcgen.org/autobuilds/pcgen-docs/index.html

Also Regan made a Ponyfinder set for Silver Games that you can buy. :)
https://www.drivethrurpg.com/product/184209/Ponyfinder--PCGen-Extension

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--Paul Grosse
--PCGen BoD, PR Silverback
@Nylanfs