I’d definately would encode to x264 and use ffmpeg’s Intel QuickSync support to save power. Encoding vp9 must be a hard workload for your small machine. Probably the video only doesn’t stutter due to interlacing. If you’d want to go hardcore, you could try to profile your task with minimal overhead by using perf record
.
You could run a 2nd sshd service with systemd where you use namespacing, chroot & drop most capabilities. (Basically a container) You can also change the default logindir of sftp. Look at https://www.redhat.com/sysadmin/mastering-systemd and
man sftp-server
.