You purchase a WP Toolkit Deluxe license for a single account. Only a single account appears as enabled on the WP Toolkit page in WHM, but a warning like this displays at the top of the page:
License overuse detected: WP Toolkit license allows 1 Deluxe accounts, but 2 Deluxe accounts were assigned. As a result of this overuse, WP Toolkit Deluxe is temporarily unavailable to all accounts on the server. You can either upgrade your WP Toolkit license to accommodate more accounts, or unassign WPT Deluxe from certain accounts.
This warning appears when multiple accounts on the server use a package whose feature list has WP Toolkit Deluxe enabled.
Either upgrade your WP Toolkit Deluxe license to accommodate multiple accounts or create a new package and feature list for WP Toolkit Deluxe, and assign only the account for which you want to use WP Toolkit to that package.