Is CloudFormation bootstrap (cfn-init.exe and friends) now compatible with EC2Launch v2 on Windows instances?

Based on the available information, it appears that the documentation you're referring to may be out of date. EC2Config has indeed reached end of support, and EC2Launch v2 is now the recommended launch agent for Windows instances on Amazon EC2.

EC2Launch v2 is the latest launch agent for Windows Server 2022 and later operating system versions. It replaces both EC2Config and EC2Launch v1, and comes pre-installed on AWS Windows Server 2022 and 2025 AMIs. It's also available for Windows Server 2016 and 2019.

While the specific compatibility of CloudFormation bootstrap tools (cfn-init.exe and related tools) with EC2Launch v2 is not explicitly mentioned in the provided sources, it's highly likely that AWS has updated or will update these tools to work with EC2Launch v2, given that it's the current recommended launch agent.

EC2Launch v2 offers more features and flexibility compared to its predecessors. It supports a larger user data size (60 KB compressed), allows for local user data to be baked into the AMI, and provides more configurable tasks at launch (20 compared to 15 for EC2Config).

Given that EC2Launch v2 has been the default launch agent for newer Windows Server versions since at least July 2020, it's reasonable to assume that critical tools like the CloudFormation bootstrap utilities would have been updated to maintain compatibility.

However, to get the most accurate and up-to-date information, it would be best to check the latest AWS documentation or contact AWS support directly for confirmation on the current compatibility status of CloudFormation bootstrap tools with EC2Launch v2.
Sources
Use the EC2Config service to perform tasks during EC2 legacy Windows operating system instance launch - Amazon Elastic Compute Cloud
Windows launch agents on Amazon EC2 Windows instances - Amazon Elastic Compute Cloud
AWS Windows AMI version history - AWS Windows AMIs