It is gibberish. The expression means:

  (1 + (x * 2)) - (3 % x)

So the correct S-exp (let's use mod for modulo rather than %):

  (+ 1
     (* x 2)
     (- (mod 3 x)))

It's a sum of three terms, which are 1, (* x 2) and something negated (- ...), which is (mod 3 x): remainder of 3 modulo x.

The expression (% (- (+ (* x 2) 1) 3) x) corresponds to the parse

  ((x * 2 + 1) - 3) % x

I would simplify that before anything by folding the + 1 - 3:

  (x * 2 - 2) % x

Thus:

  (% (- (* 2 x) 2) x).

Also, in Lisps, numeric constants include the sign. This is different from C and similar languages where -2 is a unary expression which negates 2: two tokens.

So you never need this: (- (+ a b) 3). You'd convert that to (+ a b -3).

Trailing onstant terms in formulas written in Lisp need extra brackets around a - function call.