Eric,
I hope you enjoyed your visit to Intermeccanica. Henry's team builds some beautiful cars.
You asked about the difference in the Intermeccanica Models. Intermeccanica's Pre-A 356 Speedster replicates the early 1954-55 Speedsters and also the 1956-early 1957 Speedsters (called T-1s). The primary difference is these Speedsters have Beehive style tail-lights and I believe all but the Carrera GS/GT models of Speedsters during most of that era had an instrument cluster with a Speedometer and Tach mounted on a vertical line, center of the dash, with two smaller gas/oil gauges mounted on a horizontal line with individual lights for E-Brake and low oil. This is a generalization, but it applies to how Intermeccanica builds a Pre-A. Someone will probably correct me on specifics, but I am trying to answer your Q as it applies to Intermeccanica built cars.
The 57-58 Intermeccanica Speedster (A Model) has the tear drop (cat's eye) tail-lights and the trio of gauges that you will see on most Speedster Replicas. That is the primary difference from Intermeccanica's Pre-A Speedster. Both are beautiful cars... it just comes down to your preference on tail-lights.
The Intermeccanica 356 Roadster is a close replication of the 1959 Speedster 'Vert D model. It is a much more comfortable car with the taller windscreen and Roadster style seats. These are beautiful cars and something to be considered when making your choice.
As far as the power side windows: You will find many posts on this site (do a search) by owners seeking a way to better seal up their cars due to rain, wind and cold air coming in. When there is a NEED for a side window they put up a canvas framed side window that leaks like a sieve (not a put down, just how it is). On an Intermeccanica you simply hit the hidden power window buttons and the car is now sealed from the rain, wind, or cold air. The cockpit of an IM is sealed with no air leaks (or water) coming from various places. This is another unique advantage of an IM built car vs some of the pan based cars.
I drive with the top down most of the time and almost always have the windows down.... so the "look" the above posters were referring to is the same. But, when I am traveling cross-country in the rain, on a road trip, or taking my wife out to dinner on a chilly evening, I have the option of sealing off the car at 70 mph vs stopping and inserting ineffective side windows. If a customer insists on not having the IM side windows then Henry can accomodate that. Anyway, the IM windows offer the best of both worlds... the clean look with them down (re: the above posts) and true rain/wind/cold protection when they are up.
As far as seats: Steve is right, the Roadster seats are more plush and offer more comfort (beyond the BG 800 mile seat barrier... private joke). They were installed in many Speedsters, contrary to what many people believe. IM's Speedster seats are also very comfortable, with extra seat bottom padding (this can be adjusted to your preference during the build) and both style of seats have the option of 2 stage electric seat heaters, I have them and they make a chilly top down drive quite comfortable.
Beyond the Pre-A, 57-58 Speedster and Roadster (1959 Vert D) Intermeccanica offers are the numerous choices you can make to get the car closer to the year of replication or model (Carrera GT/GS). One thing that comes to mind is the bumpers... you can opt for the High-rider bars, GT Style bumpers, or even get the bumper guards nailed down to a specfic year/style. I have the early bumper guards... a little wider. These are some of the small things that come with IM's custom builds.
Good luck in your purchase and build, Henry will treat you well and I am sure you won't regret the choice of builder. I love my Intermeccanica Speedster and think the world of Henry and his team.
PS. Check out the Registry and look at some of the different Intermeccanicas to see the variety in styles.