Thing is, everything started from anything not-Lipstick, i.e. Terminal, systemd, cron etc. etc. is per default/per design not considered by SailJail.
Only UI apps (having a .desktop file) launched via the Lipstick desktop are.
I’m rather fuzzy on the details here, but there are components like the (Lipstick/Jolla-Home) LauncherModel, invoker, and sailjail involved which parse the .desktop file, set up the Jail, DBus names, ask for permissions etc.
Now, you can replicate this behaviour by using the sailjail command line tool.
But as you can see calling that is a mix of giving the path to the .desktop file, launching the binary.
AFAIK there is no clear mapping of whatever Lipstick does to doing the exact same using sailjail (the command). I may be very wrong here however.
If there is, apps like Takeoff, or systemd services like described here may be modified to launch everything correctly.
Heck, if you must, maybe even systemd’s xdg-autolaunch-session might work.
Still all these seem a bit like hacks, and a proper API or even functionality like reading ~/.config/autostart by Lipstick itself would be much better IMO.