Riv has prettier and more intricate lugs in general. My Mercian has very plain lugwork. Mercian will however build in any lugs you like - Henry James, etcetera - and their Vincitores have fancy lugwork, but they're pricier because of it. Interestingly, if you are good at carving, you can send in your own lugs and Mercian will build them into the bike, and a customer of theirs not long ago did just that: http://www.merciancycles.co.uk/newsstory.asp?id=64

I also think the paint jobs are nicer on Rivendells than Mercians, personally, although you get what they give you. My Mercian has slightly sloppy paintwork, to be honest, although it still looks beautiful and was done with the exact colors and scheme that I asked for. The lug lining you can tell was done free-hand with a paint pen, and whoever did it wasn't the most exacting artist - it's more like they hired a cake painter to do it. C'est la vie. It's still a show-stopper of a bike, and I constantly get asked about it. Riv has the benefit of Joe Bell though, and even the bikes he didn't paint have a cleaner paint job than any Mercian I've ever come across.

The Mercians are considerably cheaper than the Atlantis, though the prices range depending on what you get done with them. Since it is a custom, though, I can see no reason for getting an Atlantis or any other production bike instead of a Bob Jackson or Mercian if you're intending on spending a grand large, especially considering the fact that you could have them completely imitate the Atlantis in every detail if you wanted, and still get it cheaper.

I really don't know what to say about comparative build quality - a lot of that is stuff that you can't see. As Grant Peterson pointed out, no person can judge how well a braze was done by looking through the paint job. I'll just say that my bike is stable, fits well, it can certainly haul a load, it handles well, and it's what I asked for.

A more intricate paint job will make a Mercian more expensive than the very cheap base price, as will adding braze-ons for racks, etcetera. As far as clearances go, on mine I had them crank out the stays to accept very wide tires and a Rohloff hub at 135 mm, so that's no problem for them at all. One thing I really liked about them was that they had some spare Reynolds 531 ST (special tourist) tubing lying around and built my whole frame out of it when I asked them to. They'll do anything you want them to, which is the point of a custom. You are no more tied down to the base model than you are tied down to toppings when ordering a pizza, unless you order one "off the shelf" from them, which in my opinion would be a stupid thing to spend a grand on and would completely defeat the purpose of going to a "bespoke" bike manufacturer - it would be like going to a master tailor on Savile Row and just buying some pants off the floor from them.

I didn't have them build an oversized head tube, but you can imitate anything Rivendell (or any other marque) does if you like it so much.

This guy had his built with a "Riv-style" oversized headtube and wide stays, for example: http://www.fixedgeargallery.com/2004/e/laumb.htm

The only thing about ordering a custom is that you'd best be sure about exactly what you want done with it, as nun so correctly pointed out. The stock chainstays will only come out to 44 cm, for example, and if you intend on putting big panniers on it, you'll want longer ones.