Those 2 tick boxes at the top of the location matching page in the wizard are independent.

‘Place any remaining unmatched locations into the location name’ – when this is ticked, the location from the import file will go into Location Name on the survey event and sample for any locations that aren’t matched to a location in the location hierarchy. Nothing will be added to the location hierarchy for these locations. Note that if location name is also present in the import file, the 2 will be concatenated. If the concatenated data is longer than 100 characters it will be truncated as Location Name on the survey event and sample is only 100 characters.

‘Use the first listed grid reference when making new entry’ – this is for use in conjunction with Make New Entry/Entries. If this isn’t ticked and you use Make New Entry/Entries for a location that has multiple grid refs in the Grid Reference column you will need to use the Centroid column to select the one you want used as the Central Spatial Ref when the location is added to the location hierarchy. If it is ticked the system will use the first listed grid reference as the Central Spatial Ref for the new location.

I will add this to the list of things to be clarified in the Help.