As an upstream spellchecker maintainer, I don't think that's a good idea. Emacs should just be using the spellchecker. If it's not working, the problem should be fixed in the spellchecker.
As far as I can see, the problem is not specific to flyspell (mea culpa for the bug title!).
For now, with current hunspell dictionaries, and using either hunspell, or enchant with hunspell backend, I have used the workaround of adding a few words like "etc" to my personal word list.
To be honest, I'm not sure Emacs can do much here. As far as I can tell, hunspell doesn't cope well with characters like "." that normally are non-word characters, but *can* occur in a word.