I use the methods here to trim files from my backup and exclude them from future backups. I have ~/.dropbox excluded, but I don't know how to delete all current backups because it's invisible (and doesn't show up when I Enter Time Machine). What's the trick to ditch invisible files' backups?
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Aha! found a way. You can view an invisible directory in the Finder by using Go -> Go to Folder... (command-shift-G) and enter the path. Once it's showing, Enter Time Machine and follow the steps here. Note: you can delete the folder you're looking at (instead of a file/folder within it) by righ/control-clicking in the Finder window in Time Machine and selecting the Delete All... option with its name there.
I'm not sure how you'd remove an invisible FILE instead of a folder though...
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Related to your question: to remove files or folders that are not even accessible to an administrative account† you'd have to invoke "Enter Time Machine" as root.
† Like MySQL log files, owned by _mysql in group wheel
