Assuming you're now using ./configure --with-archflags="-arch x86_64 -arch arm64, be sure to do a make clean; make after.

If that's not it, I'm not sure what the problem is, as that runs to completion and results in generating "fat" dual architecture executables, e.g.

$ file test/tree.app/Contents/MacOS/tree 
test/tree.app/Contents/MacOS/tree: Mach-O universal binary with 2 architectures: [x86_64:Mach-O 64-bit executable x86_64] [arm64:Mach-O 64-bit executable arm64]
test/tree.app/Contents/MacOS/tree (for architecture x86_64):	Mach-O 64-bit executable x86_64
test/tree.app/Contents/MacOS/tree (for architecture arm64):	Mach-O 64-bit executable arm64

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