Hi Mike,
The F-3100 was developed as a "sister" to the F-3000 in the late 1990's when UK framers who thought the F-3000 was a great machine (wanting to purchase one)...but then asked, "Does it cut MDF". This was the primary reason for the development of the F-3100 and of course it was designed not only with the roller cutting wheels for MDF, but also a deeper material rest for cutting thicker mount/mat boards as well.
The one key difference when comparing the two machines, is that to accommodate the MDF Channel on the right side of the center cutting channel, that portion of the anvil had to be removed. This gives the F-3000 a complete anvil and an advantage when breaking thin pieces of glass (1/8 to 3/8 inch). Breaking away larger pieces is somewhat the same on both machines.
To answer your question depends on your primary use of the machine...I would honestly say that if I was cutting primarily 3mm/5mm Foam Core, 4ply - 8ply matboard and glass, then the F-3000 is the machine that I would recommend. If you have a high percentage of MDF or thicker mat board come into your shop, then you might opt for the F-3100.
The F-3000 is sold in 48 inch (Actually the smaller model may be discontinued) and 60 inch versions (cutting height of material), while the F-3100 comes in a 63 inch version.
I hope this is helpful.
John
P.S. I own two F-3000's in my shop (the date back to the late 1980's)... Glass is cut exclusively on one while the second is used for all paper products (so it could have been an F-3100).