I wasn't aware that 'latest' in this context boils down to 'nightly'.
There is a slight misconception that must be addressed.Had this happen to me a few days ago when I've tried out latest repos to find some missing software from quarterly (since my device is made for experiments like this), and, weirdly enough, I was lucky enough for a solution to be as simple as reverting to quarterly repositories and running upgrade -f for it to see plasma packages again and successfully reinstall them. So yeah, be more careful when trying "latest" branch, cause I can't recommend anyone trying what I've tried, this was cursed lol.
The FreeBSD project is centrally managed by a team, while the ports tree is decentralized to several hundreds of maintainers.
When a FreeBSD release is made, a new branch is created — whether it's the more reliable -RELEASE (made for production), or the less reliable -CURRENT and -STABLE (meant to be tinkered with). The case is not so for the ports tree: there is only one ports tree for everything, no matter if you're using 14.3-RELEASE, or 15.0-STABLE, or 16.0-CURRENT.
When it comes to ports, while everyone hopes to make things run smoothly, in reality this isn't always the case. If things work out well, packages for all ports are built for each and every ABI/architecture. If they don't, well...
Just because snapshot releases default to the latest repository while -RELEASEs default to the quarterly repository, that doesn't necessarily mean that one is less stable and reliable than the other. You can be using latest for many years and never encounter any problem, as long as you are careful. pkg will tell you exactly what it is installing, updating and removing.
Recently, some programs depended on a newer release of ffmpeg, which meant that web browsers and multimedia players were failing to build until the right patches were made. Some users ended up updating their packages and removing essential ones in the process.
If you can find a package in one repository and not the other, it only means that it just happens that package X is still available in one and has not yet been removed from the other. If a problem persists for an entire quarter, you'll have missing packages in the quarterly repository as well. For example www/ungoogled-chromium has been failing to build for months and it's missing from all repositories if I'm not mistaken.