All seems to run well.
Just a nitpick would be to separate the alias values and possibly even the alias names with ticks or something to highlight where they begin and end. Something like the following:
$ atuin config alias set m "make run"
# Change this:
Overwriting alias m=make with m=make run
# to something like this:
Overwriting alias 'm=make' with 'm="make run"'.
I made a PR for that. Feel free to close the PR if you do not agree.