[24.2] Fix correctness of assertion validation in new linter.

[jmchilton]

We were using the YAML linters which were more strongly typed to validate the XML without a lot of processing - including no type conversion. Fixing this found some other problems also. Huge thanks to @bernt-matthias for reporting the issue - https://github.com/galaxyproject/galaxy/issues/19197#issuecomment-2498560642.

This just fixes the correctness. We still probably need a way to improve the pydantic output for these validation errors.

How to test the changes?

(Select all options that apply)

• [x] I've included appropriate automated tests.
• [x] This is a refactoring of components with existing test coverage.

License

• [x] I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.