When you uncheck the box, EasyFind shows packages, installers, apps...maybe others as "units" rather than digging into them for their components, so, yes, they "show up differently".
I don't understand why you still see 2,800 files, though. (I just d/l'ed Android File Transfer.app [Is that the correct thing?], and EF doesn't show me anything like that, but that may be because I never launched it.)
"Where" is a column heading across the top of an EF window... Name, Created, Modified, Size, Kind, WHERE.
My search criteria are the same as yours except that I search for "All Files" and check or uncheck "Package Contents" and "Invisible Files & Folders" depending upon what I'm searching for.
Command-A does, indeed, select everything, but if you hit "Delete" you'll find that anywhere from all to none of the selected items disappear; that's because the developers of EF have wisely elected to prohibit users from easily deleting files that require admin authentication.
Command-R takes you to the actual location of a file...the path shown in the "Where" column; from there you can delete files that can't be deleted from an EF window.
I think your best bet at this point may be to upload a screenshot of what EF shows you so we can get an idea of what you're up against. (I searched for an uninstaller, but with no joy.)
