As a rule of thumb anything you call from Cypress affects global state. Anything you call from cy affects local state.
Since the environment variables added or changed by Cypress.env are only in scope for the current spec file, you’d think that it should be cy.env and not Cypress.env… and you’d be right. The fact that Cypress.env affects local state is an artifact of the API evolving over time: Cypress.env used to affect global state—environment variables added in one test spec file were available in other specs—but the Cypress team wisely made each spec run in isolation in 3.0.0 and by that time Cypress.env was public API.
Further reading: https://docs.cypress.io/api/cypress-api/env.html#Why-is-it-Cypress-env-and-not-cy-env
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