kind is copied again in the for loop, right? I just want to make sure I'm reading the code correctly.

Good catch. I originally wrote the cloneNode function before @vladima modified the Node constructor, when kind was set on the prototype. I can probably drop isExcludedPropertyForClone in favor of clone.hasOwnProperty(key).

This will copy over flags and parent now, won't it? Which is bad unless they are provided by the caller.

No, flags and parent are set in the Node constructor. See line 808 of core.ts:

    function Node(kind: SyntaxKind, pos: number, end: number) {
        this.kind = kind;
        this.pos = pos;
        this.end = end;
        this.flags = NodeFlags.None;
        this.parent = undefined;
    }

And line 191 of services.ts:

        constructor(kind: SyntaxKind, pos: number, end: number) {
            this.kind = kind;
            this.pos = pos;
            this.end = end;
            this.flags = NodeFlags.None;
            this.parent = undefined;
        }

All right, sounds good.