This appears to have been an Xcode bug that has now been fixed as of Xcode 12 beta 6.

This is still happening in Xcode 12.0 beta 6 (12A8189n). I have filed a report on Feedback Assistant.

This is still happening in Xcode Version 12.0 beta 4 (12A8179i). The ProcessXCFramework step seems to copy the Header directory from each of our XCFrameworks into the same Build/Products/Release/include directory, apparently overwriting the headers from one XCFramework with those of the next. I'm not sure why Xcode would even need to create a temporary build copy of the contents of the XCFramework Header directory at all. That seems odd.