Except for editing lisp, which manipulating the AST directly in code.

Not really. The AST in lisps is much more obvious, but you're still editing a text serialisation format, and any features that operate on the AST itself are provided by the IDE on top of that.

There is no "concrete" AST that's not a "serialization format". A binary AST is also a serialization of AST.

Lisp source is pretty much as close to AST as you can get while still staying in text-land. That said, experienced Lisp developers often use tools like Paredit mode that let them navigate and edit the code in terms of tree nodes, not characters.

Indeed. Any AST in binary format is going to give version control some trouble since those seem best suited for text formats.

Macros operate on the AST at compile and run time, without any support from the IDE.

I am talking about IDEs.