Change error to warning on Universe creation

[lilyminium]

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Fixes #4750

Changes made in this Pull Request:

• This changes the error to a warning on Universe creation for types and masses guessing, which is set by default.
• Also fixes something I noticed about kwargs not getting passed into bond guessing.
• And Universe kwargs were getting passed into guessing when they're documented as being for topologies.

PR Checklist

• [x] Tests?
• [x] Docs?
• [x] CHANGELOG updated?
• [x] Issue raised/referenced?

Developers certificate of origin

• [x] I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.