GitHub charges for LFS and has since they initially introduced it, way before Microsoft was involved. Also, the pricing model is changing and will include a minimum of 10GiB for free (250GiB for Team/Enterprise customers). It’s cost-recovery and abuse-prevention, though, not some nefarious scheme. And funny you mention AWS S3... what costs might GitHub be recovering? ;)

Microsoft’s homegrown LFS implementation (in Azure DevOps) does not and has never charged for LFS. It’s nice to have friends with a cloud blob storage service!

Source: I was the product manager for Azure Repos’s LFS server and am currently the product manager for all things Git at GitHub.