While an SPC count could be helpful and you can set some limits, as noted you have a limit of <100 after cleaning. You get a count, you have limits, but what does the SPC count actually tell you around the risk of pathogen contamination of your product or cleanliness of the plant while running? I would be more inclined to test for entero as it gives a clearer indication of hygiene/contamination/soiling issues and points more towards issues around the potential for pathogen contamination to occur.
For Zone A areas (direct food contact) we test for Entero only, no pathogen testing. A positive pathogen result on Zone A will mean holding product, further testing of product etc.The entero test gives you an idea of the lines cleanliness while running.How long does your process run for?
Zones B, C & D, test for entero, pathogens(listeria/salmonella - depending on your product matrix) and yeast and moulds. As your customer noted, swab after three hours running time. Swabbing (micro or ATP) after cleaning is a validation of the effectiveness of your cleaning program, it's not showing what the microbial load is on your line while you're running and what risk there is for product contamination from pathogens and other spoilage organisms.