I have installed many ceiling fans. But many now don't have the flush mount option. I have a Hampton Bay "Sauterne" model 54" fan. It does not have the flush mount option. The canopy and motor housing holes line up the same as a fan that has the flush mount option. My question is can I flush mount it anyway, or is there a particular reason why the manufacturer does not give this mounting option?

I have no idea. To paraphrase a quote from Mike Fulk, "Try it, if it works, and does not burn your house down, then it is good."

Why was it not helpful? You asked, the holes line up, can I try flushmounting it anyway? I responded, yes you should try it. Not actually being Hampton Bay, I can't tell you what the manufacturer was thinking, nor can anyone else.