How does that affect a company like Amazon that cam claim its primary HQ in another state, and its actual realized revenue as mostly in other states? What part of Amazon's profits would get taxed in PA?

Most states have tax nexus rules where that doesn't matter as much anymore. They'd certainly pay PA corporate tax on PA income, then PA payroll on every employee.

Philadelphia has gross receipts tax. It is a no go.

So does Washington State though.

Effective rate, or published rate?

9.99% net income. It's flat so there is no "effective" rate.