I filed a bug report on this about a month ago, but thought I'd post it here as well to reach a wider audience.
So far the only 2 missing files I noticed are
include/swift/AST/. My workaround is copying/dragging these files generated by a Ninja build into the Xcode project. This works as far as my own workflow is concerned.
I know Xcode has been deprecated for building the toolchain, but it's still supported as a source editor. Among all the IDEs that I've used, imo Xcode has the best search, code navigation, quick help, etc. It'd be a shame if the workflow involving it further degrades after the deprecation, driving more contributors to (imo) lesser alternatives.