EC2 user data is the correct place to provide a bootstrap script when launching an EC2 instance because the instance processes that data on first startup and can run shell scripts or cloud init directives.

EC2 user data is consumed on the instance first boot by cloud init on Linux and by EC2Config or EC2Launch on Windows. It accepts shell scripts or cloud init configuration and is intended for initial configuration tasks. The user data payload is commonly limited to about 16 KB so very large scripts may need alternative delivery methods.

AWS Systems Manager Run Command runs commands on instances that are already launched and managed by Systems Manager and it requires the SSM agent and the appropriate IAM permissions. It is not the mechanism to supply a script that must run automatically at the initial boot.

Instance metadata is a read only endpoint that an instance queries for details such as IAM role credentials and configuration values. It does not provide a channel for injecting executable bootstrap scripts to be run at startup.

AWS Config records and evaluates resource configurations for auditing and compliance and it does not execute scripts on EC2 instances during their boot sequence.

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