As we know, we can store netmodules in assemblies instead of putting them into different files and linked them in Assembly. But as each Managed Modules have their own PE Header, CLR Header, Metadata I wonder when they are embeded into one assembly, do these headers become one complete header that describe for every managed module in the assembly or they still be separated?

.netmodules must be linked by al.exe to create a usable assembly. It's the linker's job to generate the final version of the metadata in the assembly. The one and only.
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