After reading the report, the NASA SWAT team is specifically an emergency response team for major incidents that happen at Kennedy Space Center. It's not some roving security team patrolling landing sites, etc. It makes sense to me that a highly important site like the KSC would want to have a specialized emergency response team, and KSC doesn't exactly have a large city nearby or anything like that that could provide such ERT, so it makes sense that NASA created their own.

I suspect that's the case for most of these other "unusual" SWAT teams in the article. The Department of Interior's SWAT team, for example, is part of the US Park Police and provides ERT responsibilities for highly visible national monuments, like the Statue of Liberty or Washington Monument. The HHS SWAT team is the ERT for the NIH campus in Maryland, etc.