I discovered that all the Swift libraries (libswiftCore.dylib, libswiftCoreGraphics.dylib,...) exist twice in the IPA. After decompressing the IPA, there is one version of these
I am experiencing the same issue. I have read some answers which suggest that it isn't a big deal and I have to say that it looks like it isn't.
My app contains 3 targets - main app and 2 today extensions. When I create an archive its size is a whooping 126 MB. Most of it is Swift support libraries which are about 45 MB in my case and they are included twice.
However, when I check the binary size through test flight it is 23.6 MB. Now, this is still a lot considering that my application is a simple utility.
However, it is not too much if you take into account that Swift libraries have to be included. So far I would say that even though these libraries are included twice in the IPA they are not included twice in the actual binary.
This obviously doesn't answer the original question and I am also eagerly waiting for someone to come up with the exact solution, but it might be helpful.