Steve,
First, the base is original (and may be the first that I've seen). It is an Atlas S7-442 (A, B, or C although from the photos, I can't see any differences). Sold up through 1943 or 1944, along with the M1-750 hardwood floor cabinet after 1942. In 1945, the catalog shows both replaced by the steel 9050 (which I have one of).
According to the Atlas MMB-5 manual, the serial number ranges for the four models were:
M1, MF, MH 000200 - 001344 4-STEP
M1A, MFA, MHA 001345 - 005465 3-STEP
M1B, MFB, MHB 005466 - 008123 2-STEP
M1C, MFC, MHC 008124 - ? 2-STEP
It appears that the "A" suffix was assigned retroactively, possibly as late as the time of the change to the "B". The three machines that I know of with serial numbers within the "A" range all have the 3-pulley feed chart and say just "MF" on the nameplate. Plus I know of one machine with a serial number a little above 000900 that has the 3-step pulleys. But I didn't think to ask which feed chart it has.
Anyway, I am inclined to assume because of the speed chart that the one you are looking at originally had the 4-step pulleys and that a PO changed them for whatever reason. From the photo that you posted, the machine that you are looking at appears to have the original M1-300 vise. I gave $250 for mine, with the original crank handle, and thought that I did fairly well. Price range on them is probably $200-$300. The original stand is probably in the same range, so that drops the price of the mill itself to an average of about $750. Which if the mill runs as-is and has an arbor (I think I can see it in the photo), arbor driver (can't tell) and drawbar (wouldn't be visible even if the photo were much better), is a good price.
You will want to get the 3-speed chart but otherwise, I doubt that having 12 instead of 16 speeds is a big deal.