Hi JL-MDM, thanks for the comment and Happy New Year! Just checked with our engineering team and confirmed there haven’t been any recent changes to how the Company Portal app is deployed during iOS/iPadOS Automated Device Enrollment. For enrollment profiles using Setup Assistant with modern authentication and Install Company Portal = Yes, the Company Portal should continue to install automatically as it has before.
If you're experiencing a different behavior today, that would be unexpected based on what has shipped so far. The best next step would be to gather more details about the scenario and raising a new a support request with our Intune support team via: aka.ms/IntuneSupport so we can take a closer look, as this doesn’t match any recent known or announced changes in the enrollment experience. Once a support case is raised, feel free to send me a message, so we can flag it with the team internally. Thanks!