It's right there in the article: Only patents relating to the upstream kernel are included. The "Linux System Definition" is the baseline for the non-aggression

It's right there in the article: Only patents relating to the upstream kernel are included. The "Linux System Definition" is the baseline for the non-aggression pact. The exfat system is not part of the Linux System Definition because it is not part of the upstream kernel, so it isn't covered by the non-aggression pact, so Microsoft did not include the exfat patents.