synth upgrade-system a 2nd time and that fixed it. I see that every now and then when something fails in synth and a 2nd run of synth it runs through with green lights all the way. For this particular case I can't remember if I ran portsnap fetch update a 2nd time a day later or not. I don't think I did though. synth prepare-system one more time, second time qt5-x11extras was successfully fetched instead of built, probably because its official package was updated:root@bclinton:~# synth prepare-system
Querying system about current package installations.
Stand by, comparing installed packages against the ports tree.
Stand by, updating external repository catalogs ... done.
Scanning existing packages.
vlc-2.2.1_8,4.txz VDPAU is OFF but port says it must be ON
The following packages will be fetched:
New packages to be FETCHED:
qt5-x11extras-5.5.1 (0.04% of 37 MiB: 17 KiB)
nvidia-driver-346.96 (99.96% of 37 MiB: 37 MiB)
The process will require 37 MiB more space.
37 MiB to be downloaded.
Fetching qt5-x11extras-5.5.1.txz: 100% 17 KiB 17.3kB/s 00:01
Fetching nvidia-driver-346.96.txz: 100% 37 MiB 4.3MB/s 00:09
00:00:33 => [01] Builder launched
00:00:33 => [02] Builder launched
00:00:33 => [02] Shutting down
00:02:30 => [01] 00:01:57 Success multimedia/vlc
00:02:31 => [01] Shutting down
The task is complete. Final tally:
Initial queue size: 1
packages built: 1
ignored: 0
skipped: 0
failed: 0
Duration: 00:02:30
The build logs can be found at: /var/log/synth
Stand by, prescanning existing packages.
Stand by, recursively scanning 864 ports serially.
Scanning existing packages.
No packages are required to be fetched.
Integrity check was successful.
Packages validated, rebuilding local repository.
Local repository successfully rebuilt synth status graphics/ImageMagick it didn't indicate that it was going to remove the chrome browser. As I knew the build would take awhile, I didn't supervise it after that, only to find the results printed--that it had installed this, upgraded that, and removed something else. I think, (I've seen other mention of this, but again, don't know their circumstances, and am open to the fact that they and myself have missed something), that it would be preferable to do something like portmaster does, that unless there is a -y flag (or similar), show what it will do before hitting yes or no.
synth upgrade-system? if so, until you are comfortable, only use synth prepare-system. synth install graphics/ImageMagick (which was not previously installed.) Before doing so I ran the synth status command mentioned before. Using pkg would also first say, going to install this, remove that before proceeding. I might be misunderstanding, but I thought the status option should show me that will remove something. I'm sorry I didn't note when it was removed. I started the command in another workspace then ignored it till later. (Again, I'm not positive that the status option didn't warn me. 
synth status graphics/ImageMagick or synth status? synth install graphics/ImageMagick command will first build everything (and rebuild anything) and that should match what the status command said would happen. Then, the *entire* set of packages will be scanned and validated before rebuilding the repository. It's here that packages can be removed, but these should be packages that were NOT on the status list before. synth upgrade-system behave as if I had run synth prepare-system && pkg upgrade -r Synth where pkg displays what it is going to actually do and then prompts you to answer y or n depending on if you like what you see. I assume synth just passes -y to the pkg upgrade command. Obviously if I want to do that I can use the second set of commands that I mentioned, but sometimes it's nice to just type less stuff! synth force [already-installed-port] to have a look what works and what doesn't. Those are only a few examples.
synth install <single port> could do that, especially on the ports trunk branch. It's much less likely to occur on quarterly branches.
synth upgrade-system (and synth install for that matter) is the exact opposite of what you want. And what you want obviously already exists. Pointless duplication is pointless.
Yes, thank you. I've noticed this by now and that's great. I just wasn't sure, because vermaden 's sysutils/automount is always ignored, I never knew why. Could it be because the port just consists of a script to be installed, so it doesn't need rebuilding?
04_* is skipped ports, and it just says:
sysutils/automount by sysutils/fusefs-exfat00:00:42 sysutils/fusefs-exfat: License Microsoft-exFAT needs confirmation, but BATCH is defined