Huzzah! After a little bit of grep and quite some trial-and-error, I found:

$ xinit -- vt1 -keeptty

(Side note: while this works, it uses a small corner of the screen. How to make this full screen?)

With that, I was able to use xinput list and list-prop and get the device name and properties unique to my setup. This led me to:

$ xinput set-prop 'USB Optical Mouse' 'libinput Accel Speed' -0.25

This immediately slows the on-screen pointer by roughly 25% (acceptable values seem to range -1.0 to 1.0, and default is 0.0).

Alternatively:

$ xinput set-prop 6 275 -0.25

...also works, if I were confident the device number won't ever change. I don't know what happens if I reboot, or plug/unplug additional devices etc., though, so I stick with using the name.

Now, starcraftr.sh:

#!/bin/bash xset -dpms s off s noblank xinput --set-prop 'USB Optical Mouse' 'libinput Accel Speed' -0.25 matchbox-window-manager -use_titlebar no & cd "/opt/retropie/ports/starcraft/data" && ./starcraft.sh

(The trailing & used in the example was not necessary)

This worked, but still a little fast and so I dropped it down again to -0.5. Now that feels more like what I'm used to.

Now, let's say I am a user who can't or don't want to alter the root-owned starcraftr.sh in the install folder. Or, maybe I just don't want to lose my custom setting to a reinstall. So I copy it into config dir at /opt/retropie/configs/ports/starcraft/starcraftr-slowmouse.sh, make the edits there, and then edit emulators.cfg like:

default = "starcraft-slowmouse" starcraft-slowmouse = "XINIT:/opt/retropie/configs/ports/starcraft/starcraftr-slowmouse.sh"

Fastest Settings for lr-Puae -Amiga cd32?