Isn’t “non-standard stuff” exactly what all plugins do? Otherwise we wouldn’t need them.
Sometimes pro plugins take longer to show updates I’ve found - you can usually force it by clearing the site’s transients, or you can just wait. It will show eventually.
No, plugins do non-core stuff. The ones that use the same database and functions are easily integrated with other plugins and easily migrated to using a different plugin. Those like NextGen that use their own format and functions are a hassle and don’t integrate with other plugins easily. It’s sad that plugins don’t give clues to what they are doing, and you have to look at the code to figure it out.