Extending the compiler is great... until it isn't. Imagine a feature in java the language not working correctly due to a compiler bug. Debugging or working around this issue could be very difficult. With compiler extensions, you are now widening the opportunity for this type of bug to occur.
More principled code generation systems like Racket's macro system do in fact let you expand the code to see what's generated while avoiding having a separate build step, and even have a macro debugger for interactive debugging. Mainstream languages have a ways to go before we get this kind of tooling for language extension frameworks. Until then, I think I prefer having a separate build step with on-disk, visible, and debug-able code.