No. The bolt pattern will be different only if one was out of a 6-cylinder and the other out of a 4-cylinder. If they were both 4-cylinder transmissions, they will mate up with a 4-cylinder engine.
The only thing that is series-dependent is the clutch actuation method:
The SIII has the slave mounted right through the front of the bellhousing and points aft and DIRECTLY actuates the clutch throw lever on the inside of the bellhousing. (third diagram down on this page).
The SIIA has the slave mounted vertically beside the bellhousing and pushes a bellcrank connected to a rod that runs inside the bellhousing (top 2 diagrams on this page).
If you found a SIII transmission out of a 4-cylinder, you should just be able to install it and run a line from your existing clutch master cylinder to the slave on the front of the SIII transmission (if it comes with the slave. If not, just buy one and plumb it in).
You might want to check on this, but I think the different master cylinders will work equally well with either the SIIA or the SIII slave cylinders displacement-wise.
Not all series III's had 6-cylinder engines. In fact, most didn't (besides NADA). just ask the seller if the transmission was out of a 4-cylinder rover or a 6-cylinder rover.