The FreeBSD threading was perhaps behind but in general, but the big things in Linux VS FreeBSD was always the 4.3 licensing lawsuits that gave Linux a momentum that BSD never caught up with.

The real difference during that early 00s was that momentum bought 2 things that made FreeBSD a worse choice (and made even more people end up using Linux):

1: "commercial" support for Linux, firstly hardware like you mentioned, but in the way that you could buy a server with some Linux variant installed and you knew that it'd run, unless you're an CTO you're probably not risking even trying out FreeBSD on a fresh machine if time isn't abundant.

Also software like Java servers comes to mind, came with binaries or was otherwise easy to get running on Linux, and even with FreeBSD's Linux layer VM's things like JVM and CLR often relied on subtle details that makes it incompatible with the Linux layer (tried running .NET a year or two ago, ran into random crashes).

2: a lot of "fresh" Linux developers had a heavy "works on my machine" mentality, being reliant on Linux semantics, paths or libraries in makefiles (or dependencies on things like systemd)

Sure there is often upstream patches (eventually) or patches in FreeBSD ports, those last are good for stable systems, but a PITA in the long run since stuff doesn't get upstreamed properly and you're often stuck when there is a major release and need to figure out how to patch a new version yourself.