Apple - Changing right-hand Command & Alt key order to be like a Windows keyboard

Apple's Technical Note TN2450 describes how to remap keys. It is important to know that Right Command is also Right GUI. Running the following command will switch Right Command and Right Alt (if you also want to do the Left Command and Left Alt, refer to the technical note to get the hex values and the Python code below to do the or operation).

hidutil property --set '{"UserKeyMapping":
    [{"HIDKeyboardModifierMappingSrc":0x7000000e7,
      "HIDKeyboardModifierMappingDst":0x7000000e6},
     {"HIDKeyboardModifierMappingSrc":0x7000000e6,
      "HIDKeyboardModifierMappingDst":0x7000000e7}]
}'

The table at the bottom of the Technical Note has a list of hex values for each key. To generalize the above answer to switch any keys (at least is macOS Sierra), you must or the hex value from that list together with 0x700000000. The following Python code demonstrates one way to do this.

In [1]: def convert(val):
   ...:     int_val = int(val, 16)
   ...:     ref = '0x700000000'
   ...:     int_ref = int(ref, 16)
   ...:
   ...:     return hex(int_ref | int_val)
   ...:

In [2]: r_alt = '0xE6'

In [3]: print(convert(r_alt))
0x7000000e6

A more general and user-friendly approach is to use Karabiner-Elements, which is a version of Karabiner that works on Sierra.

Karabiner-Elements allows for your specific use case (that's how I use it) in addition to almost any other kind of key remapping.

My configuration looks like