Yes, you can disregard the whole DirectX remark anyway, that didn't make much sense.
It will be just fine. FSX is not going to influence SSE, and vice versa.
It can be so, that you could have a graphics driver in use that is better for one game, yet that will not perform as well with another game, or something like that. But it's rare and in this case, that doesn't really matter.
They are not going to 'do something' to each other.
Fred