Do I have to know which netCDF file format variant is used in order to access or modify a netCDF file?
No, version 3.6 of the netCDF library detects which variant of the format is used for each file when it is opened for reading or writing, so it is not necessary to know which variant of the format is used. The version of the format will be preserved by the library on writing. If you want to modify a classic format file to use the 64-bit offset format so you can make it much larger, you will have to create a new file and copy the data to it.