.pytool/Plugin: Improve plugin log messages

[makubacki]

Description

Improves the CI output with more actionable messages and downgrades some errors/warnings.

• [ ] Breaking change?
• [ ] Impacts security?
• [ ] Includes tests?

How This Was Tested

• Verified plugin output in conditions modified

Integration Instructions

• Check if any other tools/processes depended on previous output and adjust if so.