In addition to the base of the scanner, the power and USB cables connect in the back. Although the base would probably fit on the desk, you need to allow about 1 1/4" in back for the wiring.
It will scan film negatives up to 6 cm by 22 cm. I do not know what is meant by medium format negatives. I have scanned successfully both 35 mm slides and 35 mm negative film with good results.
You can not scan directly to an SD Card. You would have to save them to your PC first and then port them to the SD Card. Maybe contact EPSON to see if the SD Card is an option.
I find that hard to believe, I was running a 4490 Perfection on the same OS, maybe you need to find the right driver. However, yes I'm currently running this scanner on El Capitan 10.11.6. It works with Photoshop, Acrobat, Image Capture.