Well first off, you have like a bajillion inches worth of spacers AND your stem is at a positive angle. If you want your bars to be lower than your saddle all you have to do is place the spacers on top of the stem instead of below it, and then flip your stem.

I work at a bike shop and from personal experience I have seen some customers that need their saddle really low even with the proper leg extension. For people who are chubby/heavy set the problem seems to amplify drastically.

I agree with the fitter that a 54 would be too cramped for you. If it bugs you that the saddle is so low... do what I said and just flip the stem and slam it.