Miscellaneous cleanups (#23048)
### Description
<!-- Describe your changes. -->
- fix some missing end of version markers and since_version info
- fix include to use onnx_protobuf.h which handles minimal builds
- we should always prefer that header over directly using the onnx ones
### Motivation and Context
<!-- - Why is this change required? What problem does it solve?
- If it fixes an open issue, please link to the issue here. -->
