I still fail to see what exception you are referring to. As a great-grandson of the Queen in collateral line, Archie is not eligible to become a prince now. The same rule will apply e.g. to the children of James, Viscount Severn, who will also be great-grandchildren of a sovereign in paternal line. The difference is that Archie, unlike James' future children, can still be a prince when Charles ascends the throne, as he will be a grandson of a sovereign, even though James himself and his sister Louise, who are also grandchildren of a sovereign in paternal line, just as Archie will be, do not use the HRH themselves, despite being entitled to do so.
Of course, other great-grandchildren in maternal line of the Queen, like Peter's and Zara's children, or Eugenie's and Beatrice's children/future children, are not titled either and will never be according to existing rules.
The only great-grandchildren of the Queen who are indeed treated differently (I am not sure if that could be called an "exception" though) are indeed William's children, but their situation is actually different, in a system based on hereditary succession under the rule of primogeniture, because they are in direct line to the throne. The rule of primogeniture, as foreign as that concept may be to most Americans, implies a natural hierarchy in any Royal Family and it is not unnatural, nor shocking to most Europeans that the main line and the collateral lines should be treated differently.
In a slimmed-down monarchy, you might argue that no grandchildren of the heir should be HRHs (only his/her children), which is the current rule again e.g, in the Netherlands and in Spain, but asking for the contrary, i.e. that all grandchildren of the heir be HRHs would again attractive negative reactions. In fact, as far as I know, Belgium is the only European kingdom where all grandchildren of the heir are still guaranteed to be HRHs from birth.