I don't know anything about Apple's associated domains feature, but it looks like your workaround may be to use a custom domain for SES engagement tracking URLs, or disable engagement tracking on the messages/URLs that need to comply with Apple's program.

https://docs.aws.amazon.com/ses/latest/dg/configure-custom-open-click-domains.html

In order to address the issue with universal links not being recognized due to SES wrapping links for click tracking, we can follow below steps :

1. Disable click tracking for the specific universal links by adding the ses:no-track attribute to those link tags in the email HTML. For example: <a href="https://example.com/universal-link" ses:no-track>Universal Link</a>

This will prevent SES from modifying those specific links, allowing the universal link format to be preserved. [1]

2. Disable click tracking entirely for the configuration set used to send the emails containing universal links. You can do this by modifying the event destination settings for that configuration set to exclude the "Click" event type. [1]

With either approach, the universal links should work as expected on iOS since SES will not modify those URLs. However, you will lose click tracking capabilities for the links where tracking is disabled.

I would also like to inform that you can try to configure a custom subdomain to handle open and click tracking instead of using the default awstrack.me domain. By setting up a custom subdomain [2] and configuring a SES configuration set to use that subdomain for tracking [2], SES will replace links in emails with your custom domain rather than awstrack.me. You can test the custom domain and check if it helps to resolve the issue.

Reference

[1] Amazon SES email sending metrics FAQs - Amazon Simple Email Service  https://docs.aws.amazon.com/ses/latest/dg/faqs-metrics.html

[2] Configuring custom domains to handle open and click tracking - Amazon Simple Email Service  https://docs.aws.amazon.com/ses/latest/dg/configure-custom-open-click-domains.html