The workaround is actually setting wantobjects to 0, which I doubt
everyone will like. 
I've talked with a tcl developer and some interesting points were raised
from the talk:

1) Looking at typePtr in _tkinter isn't actually good (this is used to
convert the tcl object to a proper python object), because it may not
work always, like in this case. But the person also mentioned he didnt't
know of any good solutions to that problem.
2) Cause of the problem -- most likely: something else in the code that
creates the message box is using the literal string "5" as a
-borderwidth or a -padding or as something else that's passed to a
widget. And the compiler uses the same Tcl_Obj * for that "5" and the
"5" that you pass to [tk_dialog].

Apparently trying to fix this in Python would case some (major?) changes
in _tkinter.