Running a command as a specific user on an ec2 using ssm
I didn't find anything on AWS or boto3 docs that allows for that, but I was able to execute as a different user using the runuser command. In theory, you could do the same thing with a combination of sudo and su commands, but this one is pretty simpler.
For that, you can do as follows:
runuser -l  userNameHere -c '/path/to/command arg1 arg2'

Since send-command executes as root, you don't have any issues.
Note: I thought that send-command uses in some way a session managed by the SSM Session Manager, but I was wrong. I spent a good time configuring SSM Session Manager preferences and tagging IAM resources according to this doc and this one, but send-command always execute as root as far I saw.
Sources:

https://man7.org/linux/man-pages/man1/runuser.1.html
https://www.cyberciti.biz/open-source/command-line-hacks/linux-run-command-as-different-user/