Hi Catlin I read your post and what you described well I would think about it for a second. Fitting a bike like the Fargo is a different matter altogether than fitting a road bike. The Fargo is like the bike version on an old Toyota land cruiser. And there are some very big differences in the way one sets up a drop bar 29er vs a road bike (google it to see pictures). For one a drop bar 29er's are not designed to ridden on the hoods but in the drops giving you better control in the dirt. So the bar sits up MUCH higher than on a road bike (in relation to the saddle and top tube) Which brings them closer to the rider. On any touring bike and especially one designed with off road as its primary purpose you don't want to be as far forward on it as you would a road bike. The riding position is almost up right the reason it pretty simple riding a long way and on rough roads will kill your lower back, shoulders and wrists in a race tuck position. Secondly the head angle is 70 degrees on the Fargo which is wicked shallow most road bikes its the the range of 72-74 ( and mountain bikes its 72-71) which means the bars are closer to the rider the shallower the angle. Also a 120mm stem for smaller riders is well I'm not sure what to call it but retarded comes to mind. Long stems like that are are rarely used on bikes out side of those belonging to huge men where the largest frame is still to small. OR for people who bought a frame that was too small to begin with.
As for the seat post the 73 degree angle really isn't that big of a deal, your talking a few millimeters difference depending on how long the seat tube and seat post are and for small riders it isn't that much. Like wise it can be over come with a zero off set seat post like a Thomson Elite and I would strongly recommend a Brooks saddle for any touring bike which are not only super comfortable they have really long seat rails and will more than likely out last the frame I've been riding the same saddle for almost 15 years. I have ridden the Fargo and the bike has a very long wheel base which makes it stable but slow to turn Fargo comes with a 90mm stem stock so a 80mm stem isn't going to tighten up the steering that much you'd notice and might even be better if you hit single track.
As for stand over height well 1 cm is not a huge difference a good touring shoe (one you can walk in will make up that difference.) Because you want a shoe you can walk in with out trashing the cleats on a tour trust me you'll end up walking a lot on tour.
SO I guess my point is Bike Shop employees make commission and will always try to up sell you from an $1800 bike to the $4000 dollar custom job because it fattens their pay check. And the fitting guy was fitting you for a road bike not a off road 29er touring bike or even a touring bike. Most shops don't really have any idea about touring because the focus in the industry for the last 20 years has been all about performance. Touring isn't about going fast its about going a very long way comfortably. So touring is a small niche thing and the shops that focus on it tend to be run by old grumpy men with white beards who drink a lot.
As for a new bike even a custom one is going to take a bit of adjusting to make it feel right.
Just saying as a guy who turn wrenches for a living and hates it when I hear people get bad advice on a bike fit. Or told no to something they want. I mean if the Fargo is the horse that sings to you don't be swayed by some 12 an hour bike shop snob. Go find a shop run by an old guy with a white beard and sorta smells like axle grease and Jack Daniels he'll have it in stock and go ride it and see how it FEELS because all the fancy measuring won't tell you how a bike feels and you'll be able to tell right away if its going to work for you or not. So there is no need for sad days. Hope my 2 cents will help you out.