But if the syntax is arbitrarily customizable, you can't possibly have the tools understand how to highlight it / intellisense / autoindent / etc.
It's trivial. Any PEG parser I add on top automatically communicates all the highlighting, indentation data and all that to the tools (and it's inferred from the declarative spec, no additional user input is required). Underlying typing engines do the same, for the nice tooltips and code completion. The very compiler core doest the same with all the symbol definitions, dependencies, etc. Easy.
The way you express DSLs is something that needs to be understood by language tooling, so it belongs in the language spec.
So, in your rot13 example compiler would rat all the new identifiers with their origins to the tools.
How can the compiler know which identifier connects to which origin, unless because the macro complied with some standard/restriction/protocol? From a certain perspective all I'm suggesting is making these protocols part of the language standard - that is, define the DSL that's used to define DSLs, rather than allowing macros to consist of arbitrary code.
I've got some code published, but not that much in writing, planning to fix it some time later. See the stuff at my github account (username: combinatorylogic). Relevant things there are Packrat implementation, literate programming tools and an Emacs mode frontend.