I bundle swift command line tools with my apps, and I was able to work around this by pointing them to the Frameworks folder of my app bundle. If the command line tools are in your resources folder, you can point "Runpath Search Paths" to @executable_path/../Frameworks/.
I also needed to add an additional swift framework to my main bundle's frameworks. Dragging in /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/swift/macosx/libswiftSwiftOnoneSupport.dylib to the frameworks list did the trick. Running a test swift 5 command line tool in macOS 10.13 gave me a Hello, World!