The short answer is you really have to strap them on to find out what scale length and body shape fits you the best. Since I'm not one for short answers, here's the rest of my thought...
I pretty much had to play them. I started wanting to get a custom back about eight months ago. At that point, I did two things. One, I started a search for used instruments that were in the ballpark of what I thought I wanted. Two, I went to the local and not-so-local dealers to put my hands on Alembics.
While there isn't an Alembic dealer on every street corner, hopefully there's one in your vicinity. I have no idea where you are located, but I can say that just about anyone in the US can afford a 3-4 day weekend trip to Florida. With airfares under $150 round trip, a getaway to Orlando puts you at Bass Central where they have a tremendous stock of new Alembics. I was fortunate to get down there, as well as have my company fly me to Seattle for a few days where I was able to stop in at Bass Northwest. Then, there's a trip to Santa Rosa to the factory itself, with another dealer down around San Jose somewhere. In short, if you can afford to spend the $5K+ you're likely to put into a custom Alembic, you can probably afford to spend a few hundred on a short vacation that will help you get it right.
In my search for used basses, I ended up buying a couple of older Alembics to play with for a bit. The first was a '90 Persuader five in medium scale. The second was an upgraded '82 Spoiler with new Signature electronics. I have enjoyed playing both of these instruments and expect that I will be able to sell them for what I paid once my custom order is delivered. Also, if you get really lucky with your used purchase, you may decide that you can be happy with it and save money over the custom route. Worst case, I figured I would eat a couple hundred dollars to buy and resell a bass that didn't quite fit me. Again, this is pretty cheap compared to what a mistake on a custom order would cost you.
Playing all these basses, here's are the opinions that I developed:
1. A 32 five string can sound great, though I believe that heavy neck woods are critical here.
2. I am faster, cleaner and more comfortable on a 32 than a 34. With four strings, a 30.75 is even better, though I wouldn't gofive strings at short scale.
3. The stock pickup position on an SC bass is pretty tight sounding, but moving the neck pickup closer to the neck warms it up.
4. Even the most simple electronics package with a filter has amazing tone shaping possibilities.
5. I prefer vol/vol to vol/pan. I have no idea why.
6. The regular string spacing on a Signature bass is too wide for me on a 30.75 scale, but it's okay on a longer scale. Also, spacing that felt too wide became comfortable with more play time.
7. 10 year old basses with brass hardware look a bit beat if not well cared for.
So, what does this mean in terms of custom options:
1. I wouldn't consider a bass that doesn't at least have Purpleheart neck laminates.
2. Body shape, scale length and neck dimensions are personal things. No one else can tell you what you will feel comfortable with. You can try to guess as a comparison to basses you have played, or you can seek out things closer to what you think you want.
3. I would pay the extra for plated hardware. If you're planning on having the bass a long time, it will stay nicer looking down the road. You won't get your money back on it if you sell it soon, though.
4. Everyone who has LEDs loves them. Maybe it matters, maybe it doesn't, but I was swayed.
You're going to be spending a lot on an instrument to custom order. If you're not doing it to own for life, you probably shouldn't do it. If you are, then get the cosmetic options that will please you. A few hundred extra to make the bass more special to you will be worth it over 20+ years.
All this is my personal opinion, certainly there are others who will disagree with things I have written above.
Good luck-
Bob