fix: flags omit undefined for boolean flags

[mshanemc]

fix #729

[boolean flags have a built-in parse function even if the user doesn't specify it. It was easier to filter out undefined flags after calculating all the valus than to try to interfere with boolean flags before the default logic happens]

[WillieRuemmele]

QA Notes

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✅ : NUTs
✅ : git checkout main src && yarn build && yarn test which will validate that the new test is correct
✅ : all UTs pass