So there is a little clause you may have missed:

Type checking requires spread elements to match up with a rest parameter.

Without Rest Parameter

But you can use a type assertion to go dynamic... and it will convert back to ES5 / ES3 for you:

function foo(x:number, y:number, z:number) { 
 console.log(x,y,z);
}
var args:number[] = [0, 1, 2];

(<any>foo)(...args);

This results in the same apply function call that you'd expect:

function foo(x, y, z) {
    console.log(x, y, z);
}
var args = [0, 1, 2];
foo.apply(void 0, args);

With Rest Parameter

The alternative is that it all works just as you expect if the function accepts a rest parameter.

function foo(...x: number[]) { 
 console.log(JSON.stringify(x));
}
var args:number[] = [0, 1, 2];

foo(...args);

TypeScript can fairly easily represent prepending a type onto a tuple type, called Cons<H, T> like this:

type Cons<H, T extends readonly any[]> =
    ((h: H, ...t: T) => void) extends ((...r: infer R) => void) ? R : never

type ConsTest = Cons<1, [2, 3, 4]>;
// type ConsTest = [1, 2, 3, 4]

You can use this definition along with conditional mapped tuple types to produce a Push<T, V> to append a type onto the end of a tuple:

type Push<T extends readonly any[], V> = Cons<any, T> extends infer A ?
    { [K in keyof A]: K extends keyof T ? T[K] : V } : never

type PushTest = Push<[1, 2, 3], 4>;
// type PushTest = [1, 2, 3, 4]

but this definition of Push is fragile. If the T tuple has optional elements, or if it comes from the parameter list of a function, you'll notice that the compiler "shifts" the optional markers and parameter names one element to the right:

type Hmm = (...args: Push<Parameters<(optStrParam?: string) => void>, number>) => void;
// type Hmm = (h: string | undefined, optStrParam?: number) => void

Parameter names are not really part of the type so while it's annoying it's not affecting the actual type. Appending an argument after an optional one is... strange, so I'm not sure what the right behavior there. Not sure if these are dealbreakers for you, but be warned.

Anyway your AugmentParam would look like:

type AugmentParam<F extends (...args: any[]) => any, ExtraParam> =
    (...args: Extract<Push<Parameters<F>, ExtraParam>, readonly any[]>)
        => ReturnType<F>

and it works (with the earlier caveats):

type F = (x: number) => boolean

type F2 = AugmentParam<F, string>
// type F2 = (h: number, x: string) => boolean

type F3 = AugmentParam<F2, boolean>
// type F3 = (h: number, h: string, x: boolean) => boolean

Okay, hope that helps. Good luck!

Link to code