It depends on what you mean by "user data bootstrap."
If you are referring to the instance's user data, that is fetched from the instance metadata service, which requires no rules because its IP address, 169.254.169.254 is subect to special rules.
Amazon security groups and network ACLs don't filter traffic to or from link-local addresses (169.254.0.0/16) or AWS-reserved IPv4 addresses—these are the first four IPv4 addresses of the subnet (including the Amazon DNS server address for the VPC).
https://docs.aws.amazon.com/vpc/latest/userguide/VPC_Security.html
User data (in this sense) is passed to the EC2 service API when the RunInstances
Action is called, to request that the instance is launched. The EC2 service stores the user data so that the instance can fetch it from the instance metadata service after it starts. This prevents the instance from needing to fetch it externally.
If this is what you are referring to, no security group configuration is necessary.
See also What's Special About 169.254.169.254?
But, since you mentioned PaloAlto, it looks like you might also need access to an S3 bucket, based on this:
The management interface of the VM-Series firewall must be able to access the S3 bucket to complete bootstrapping. You can either assign a public IP address or an elastic IP address to the management interface so that the S3 bucket can be accessed over the Internet. Or, create a AWS VPC endpoint in the same region as the S3 bucket, if you prefer to create a private connection between your VPC and the S3 bucket and do not want to enable internet access on the firewall management interface. For more information refer to the AWS documentation on setting up VPC endpoints
https://docs.paloaltonetworks.com/vm-series/7-1/vm-series-deployment/bootstrap-the-vm-series-firewall/bootstrap-the-vm-series-firewall-in-aws
A VPC Endpoint for S3 allows you to not only access S3 (within the same region as the endpoint) without going out an Internet Gateway, but also to restrict the instances using the VPC endpoint to accessing only specific buckets and performing specific actions. This is the only effective way to control restricted access to S3 as a whole, because otherwise it must be accessed via the Internet and its IP addresses are not static and thus can't be referenced in a security group. Even if IP-based restriction were possible, it would provide no meaningful security since data exfiltration could be accomplished by a malicious user, using their own bucket, since you'd be allowing connectivity to all of S3. There is no correlation of IP addresses to specific buckets.