I have found the problem, when you add your data you update the contents.xml file you add your data at numbers 1 & 2. All marketplace airports are added at -100 and any airports in the community folder are added at 0, therefore you will always overwrite a 3rd party airport. If you want to overwrite only the base data you need to change your values to anything less than -100
The other option is to start your airport with any letter higher than a N that way due to the 2nd way scenery is loaded it will load after navigraph-navdata. Maybe you could pass this onto your team.