Posting a solution for those who might encounter the same issue.
As per the suggestion mentioned in the bug report linked in my original post, starting from MacOS Sequoia, the Maintenance Tool app bundle needs to be signed and notarized separately (unless this is fixed in Qt IFW > 4.8).
Fix steps:
use the binarycreator to generate a Maintenance Tool (use your preferred config.xml)
sign and notarize the Maintenance Tool yourself
implement the logic of replacing the tool as per the Qt IFW documentation in your installscript.qs (provided in previous post)
distribute the Maintenance Tool as other packages (your logic may vary here)
additionally, you may need to elevate the Maintenance Tool's permissions by executing a chmod +x operation (can be done in your XML config)