That one can expand macros does not make them non-existing. The programmer writes the macro forms, not their expansions.
If you actually look into the R5RS document, you can see that chapters 7.1.3-7.1.6 define the syntax for that particular toy version of Scheme.
Lisp usually has three syntax types: function applications, built-in operators and macro operators.
That you can implement some constructs by expanding them to LAMBDA expressions says nothing about the syntax of Scheme or Lisp. Lisp users don't develop in pure lambda calculus. Each built-in operator and each macro operator are adding syntax.
One can reduce arithmetic to lambda expressions - this does not mean that Scheme has no arithmetic operators. R5RS documents arithmetic and not their lambda variant. Same as R5RS defines the syntax for DEFINE, COND, IF, CASE, SYNTAX-RULES, ... That's what the progammer sees, not LAMBDA.
Take any real world Scheme, like Chicken Scheme -> lots of macros have added syntax. That's what the programmer uses, not lambda calculus.