I bet it was rather CBP directly who flagged him.
They have his address in a database for a trusted traveler program.
They were the ones who intercepted the shipment.
They checked the destination address on the shipment and cross-referenced it.
I'm not sure how Rimowa would be involved, frankly.
We don't know if they were involved, but it's possible Rimowa knew who the exporter was (from seeing the fakes online and ordering one themselves) and CBP then seized the package when it was imported. The article says, "Reed never received the suitcase" which indicates that the shipment could have been seized upon entry (because they were tipped off by Rimowa to look for packages from that exporter). Now they knew who the importer was (Reed) and they added his name to a database of illegal importers.
Since it was just one suitcase, it probably wasn't worthwhile going after him, but now his name was in the database (likely because they think it will help them catch more illegal imports). The tricky problem arises because there is likely no distinction in the database between one guy who didn't know he was ordering one counterfeit product for himself versus someone who imports container after container of counterfeits for resale. CBP enforces the law by seizing the product and it's up to the company to sue the importer. It's clearly a broken system with nasty ramifications for the people who got scammed.