Sometimes! There's a toggle that the IRS can set on their end, to either check the entity type against their database or to not check. If they aren't checking, the return will be accepted. If they are checking, the return will be rejected. No way to tell which way it's set other than to e-file.

Since a calendar year 1120S being filed now is delinquent, I suspect they're currently checking. It's usually turned off right before filing / extension deadlines.