SwiftPM supports to specify custom header directories with .headerSearchPath with target directory relative path. It adds -I options to compiler arguments.
"swift package generate-xcodeproj" also adds them to HEADER_SEARCH_PATHS, but it just add it as -I./Headers, which is not resolved as target directory relative path.
I think SwiftPM should set HEADER_SEARCH_PATHS with $(SRCROOT)/Sources/Example/Headers.
One temporary workaround is creating a symbolic link of Sources/Example/Headers in project root dir. (like https://github.com/swiftwasm/wamr-swift/tree/aa2991edaf43bc6301972fb3d16c731dad71d25c)