The important question here is how does that gasket "match up" the the headers you're using? If this is that same 350 you were asking about the cam/lifters, I'd say those "holes" are too big. The headers may be as well. A 1 5/8" header is called for. Felpro's header gasket for the d-port fits Hooker "Comps" and other smaller-tube jobs very nicely.
If the headers ARE 1 3/4" or larger, all is not "lost". The edge of the port that "hanging" in the flow path acts as a "reversion dam", helping keep things going along. So, while not "optimum", not nearly as bad as the reverse situation (header flange hanging into flow path).
Agreed, unless you ARE using headers, do NOT use header gaskets. The steel shims that come in full gasket sets work well with Pontiac manifolds.