"Multiple paths" "Missing paths" "Commit can not be parsed" warnings when bootsrapping monorepo manually

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- What you're trying to do
I have a monorepo that I'm trying to [bootstrap manually ](https://github.com/googleapis/release-please/blob/main/docs/manifest-releaser.md#bootstrap-manually)and cut a release PR. I created a `release-please-config.json` with all the subpackages and a manifest with initial versions. When I run the release please command for the first time, I get warnings/errors that I don't understand. The PR is successfully created but I'm wondering what the warnings mean.
- What code you've already tried
This is the [`release-please-config.json`](https://github.com/unjust/bootcamp/blob/3dc4ddd49f3281ba50784249fbd459e350ff60cb/release-please-config.json)
This is [the manifest](https://github.com/unjust/bootcamp/blob/3dc4ddd49f3281ba50784249fbd459e350ff60cb/.release-please-manifest.json)
This is my command to cut a release
`release-please --token= --repo-url=unjust/bootcamp --target-branch=bootstrap_release_please_1385 release-pr`
- Any error messages you're getting
Full output here https://gist.github.com/unjust/5ff960565bd466b72f7f8fcbae14323b
But I'm confused by:
* the [various Multiple paths warnings ](https://gist.github.com/unjust/5ff960565bd466b72f7f8fcbae14323b#file-output-txt-L46-L49) which only seem to be in the packages that are `simple` projects and not node
* [the `Missing paths` message](https://gist.github.com/unjust/5ff960565bd466b72f7f8fcbae14323b#file-output-txt-L69)
* and [various non parseable commits](https://gist.github.com/unjust/5ff960565bd466b72f7f8fcbae14323b#file-output-txt-L191-L204), which majority seem to be commits on that target-branch

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