Code block in Fusion Builder

Media cleaner is something I’ve been looking for for a while now. Our site has gotten a bit out of control when it comes to old images.
After taking several days to figure out the right settings for our server, we found out that while this plugin does somewhat work with the fusion builder, it didn’t seem to check the theme options (for our logo and favicon) or the code blocks. The theme options isn’t a huge issue, but I use the code blocks so much in page development to place images that I can’t really trust the list this plugin gave me at all.
Is this something that will be fixed in the future? or something I can do to get around this?