Small correction: PharoJS transpiles to JS in general, not only at deployment time.
Also one can easily get the impression that Amber is better suited than PharoJS. But there is no ultimate winner. They have different approaches and which to choose should depend on your problem.
PharoJS can have some benefits:
1. PharoJS has more to offer for development as you can use the whole Pharo toolset to boost your productivity. Amber currently has only basic tools like Browser, Workspace, TestRunner, … and the community is too small to reimplement all tool suites
2. PharoJS allows you to develop on regular machine while having the target app running on a browser in a mobile device in a lively way. Would be hard with Amber — as phones are too small to develop on them.
There are also other approaches like SqueakJS — which can even run a full image in the browser following the traditional “work on one, deploy on the other” approach of Smalltalk.