As good as Swift is, putting it by default in asinine paths like "/Library/Developer/Toolchains/swift-latest.xctoolchain/usr/bin" doesn't help anybody (and a ton of stuff in OS X is like this).
A more Unixy way to do this would be /opt/swift-3.0/bin, where /opt/swift is a symlink to /opt/swift-3.0. Even Apple used to limit the path insanity to merely /Developer/usr/bin. Not sure what happened...
# xcrun --sdk iphoneos clang [...]
# xcrun --sdk iphoneos --find clang
You're not supposed to remember those paths. Xcode and xcrun remembers them for you.
Apple doesn't touch the base OS folders for non-OS software, which is why stuff goes into /Library and /Applications. Besides, (Apple has never used /opt, and doesn't even document it, last I checked: "man hier" doesn't mention it.)
This could cause entertaining problems for people who routinely install both current and beta versions of dev tools (which is relatively common; if you're working on iOS10 features for your new app but still need to release iOS9 updates during the beta period you more or less _have_ to, for instance). I suspect that's why they changed it in the first place.