We (Mozilla) store our SOPS-encrypted files in git repos and we don't really get merge conflicts, but that's just because we structure secret files in a way such that two people don't edit the same file at the same time often. Git history is also fine. Have you considered configuring SOPS as a differ for git?
SOPS is fine, I was more referring to my implementation.
The reason my pipeline scales poorly is because it requires a full build and deployment cycle to update my dev / stg / prod configurations.
Also, if you store the encrypted files in our git repos as I do, you get constant merge conflicts and basically useless git history.
It is an extremely lazy implementation and literally the bare minimum I could do to get get my application configurations updating in my CI/CD stack.