This does not sound like any issue a standard plugin or theme that deals with images or featured images will ever be interested in dealing with, at least from what I can gather from what you described.
If I understand, you have some plugin or other mechanism that will insert images from custom fields somewhere into a post as a post-processing procedure – after the post has been generated and processed by the normal system routine.
Featured Images are handled completely separately from any other image in a post and are 100% up to a theme to add to posts. This is normally done as the post/page is being generated.
Show Posts uses standard WP post API calls to generate the content of a post – including inserting a designated Featured Image specified for the post. There is no special treatment for the first image in a post/page.
So if a plugin is adding images specified in Custom Fields AFTER a post has been processed, then there is no theme or other plugin that will find or know anything about such images.
I don’t know if that is what your are really asking, but as far as I know, there is to way to add in images from custom field values that will for sure be found by the theme or plugin actually generating the html output of a post/page.