A motivation for considering general schemes is to put algebraic geometries over different base rings into a single type theory, where different base rings can be simply interpreted as different contexts! For the reason why beyond finitely presented, an example is $\mathbb{Q}$ over $\mathbb{Z}$, which is not finitely presented, and we need to include $\mathbb{Q}$ in the "universal" $\mathbb{Z}$-algebraic geometry if we want to describe $\mathbb{Q}$-schemes in it.
In Foundations, the definition of schemes is restricted to those which are quasi-compact, quasi separated schemes, locally of finite presentation. However, as mentioned in Blechschmidt 21, pp 144, 153, if we choose to build the zariski topos based on f.p. algebras, we cannot even include $\mathbb{Q}$ in the $\mathbb{Z}$-algebraic geometry!
And furthermore, what are the difficulties to go beyond finite presentation in SAG?