This article explains that most of the payment methods are not displayed on checkout when multiple shipping addresses are specified, because the functionality is only implemented for Cybersource.
The core Adobe Commerce Cybersource payment integration is deprecated since 2.3.3 and will be completely removed in 2.4.0. Use the official extension from marketplace instead.
Prerequisites: In the Commerce Admin, enable and configure PayPal and Cybersource payment methods, and enable Multishipping for your store.
Steps to reproduce:
Expected result: PayPal and Cybersource are available as payment options.
Actual result: Only Cybersource appears as available payment option.
Currently Cybersource is the only supported live payment method for multishipping checkout, starting from version 2.2.4. Support for multishipping will likely be built for each payment method one by one. No exact dates or release numbers can be provided at the moment.