If systemd is condifured to not start transmission at boot, checking it's status will show something like this:
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pi@rpi:~ $ systemctl status transmission-daemon.service
● transmission-daemon.service - Transmission BitTorrent Daemon
Loaded: loaded (/lib/systemd/system/transmission-daemon.service; disabled)
Active: inactive (dead)
If that's the case, then setting it to start at boot is easy:
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pi@rpi:~ $ systemctl enable transmission-daemon.service
If it's not that though... then I'm a bit short on ideas! You could try "reenable" instead of "enable" which is meant to disable and then enable to ensure the symlinks sytemd uses are correctly set up.