Hi @lockheed I have a few suggestions.
Rather than play around with individual startup entries (which end up being desktop files in ~/.config/autostart as @anon42388993 mentioned) I add exactly 1 startup.sh file then edit that script as needed. Your xinput and xrandr commands can go here and adjusted with nano.
Another thought is the ssh -X option. You can run X on individual apps like mate-settings. I do this all the time for synaptic and gparted to a server with no desktop environment at all. Of course, you need X running on both ends. When I install synaptic on the server it installs enough X to work fine.
Last, after years of xinput commands in startup, mostly to tame a wild mouse, I moved it all to /usr/share/X11/xorg.conf.d/60-mymouse.conf. More like the old days.
Just my 2 cents