I personally take the approach regarding places that if the nature of one level renders the level above it ambiguous then then ambiguous level should be eliminated not left blank. However, census records and tax roles are very acurate so these can be used to hint at the actual location. So if a church for a baptism is only located in Hatchville, WI, USA but the tax roll or census places the building or neighboring building in a particular county, then you can satisfy your need for a county by using this additional information.
But unless it is real important to know the exact county or township I would skip it. Because the reality is:
1) Saying Hatchville, WI, USA is probably enough for an accurate "jurisdictional" place, since IF the county was jurisdictionally important the information would have been recorded.
2) Your mapping software will find the community without the additional data.
And you can still record a note that states Hatchville, WI is in multiple counties.