MTO vs. Custom is a point of confusion on SF sometimes. MTO (made-to-order) is when they have designed models that don't get made until you order them. Custom is when you get to specify your order's details.
Rancourt offers pre-made, MTO, and custom. MTO are what you see on their website fully fleshed-out and the same price as pre-made. They are about $50 or so cheaper than if you ordered the exact same model as a custom order. However, once you jump to a custom order, you can flesh it out however you want, change the eyelets, change the lining color, mix/match colors of shell, anything where they have the materials. At that point, they only charge a little bit more if there's a difference in material cost. There's also a difference in returns/exchanges, because Rancourt can kind-of assume that with MTO, someone will order that same pair of shoes in your size at some point, and with ready-made they can be really sure. They can't assume that with custom.
What Allen Edmonds offers with their SF discount is custom shoes, you can get your shoes done however you want, without the usual custom order charge (so instead of $595 for shell + $150, it's just $595). On top of that, they don't charge any extra if there's a difference in material cost. So, you can order to your heart's content premium linings, double JR soles, different stitching, etc. AE also offers pre-made (of course) and MTO (sometimes you see that a model will be shipped to you in 3-6 weeks). And, the real kicker is that when they have a company-wide sale (like RDA 15% off) it will stack on the SF discount.
While I'm at it, Quoddy is often brought up. Quoddy *only* offers custom shoes to individuals, though they offer suggestions that make it seem like you are ordering MTO. If you call up Quoddy, they will make any alteration that is possible, at no extra charge. For example, I got a pair of camp mocs that shouldn't have come with a saddle with a special very interesting saddle put on, at no extra charge.
For what it's worth, I've used all these services. I have one custom CXL Rancourt boat shoes (three eyelets, back when MTO and Custom were the same price), one MTO CXL Rancourt ranger, one MTO shell Rancourt beefroll, and one Custom shell Rancourt ranger. I also have 2 custom shell AEs on their way. And I have 1 custom chromepack Quoddy. In my experience, all three have been excellent at helping me design my shoes.