Hi, @Vid3al
Thank you for posting in Microsoft Q&A forum.
They are two different features but they are used to manage and deploy third-party updates, the difference is "Third party updates" can not create custom catalogs.
For more details, you may refer to:
https://learn.microsoft.com/en-us/answers/questions/1419231/scup-end-of-life-whats-the-replacement
You do not need to disable the "Third party updates" from SUP before upgrading MECM to version 2403.
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