For reasons unknown, Microsoft is ignoring the Mac version of the IntelliType software, even though they still regularly update it for Windows.
The only way to get it to work in El Capitan or later is to follow the instruction in this topic. Not everything you need to do is in one response, so here's all of it together.
1) Boot to the Recovery partition, or a flash drive El Capitan installer you've created. Click Utilities on the top menu bar, choose Terminal and enter:
csrutil disable
Restart normally back to El Capitan.
2) Install IntelliType. You'll be told it's an unsigned app if you double click the installer. So right click on it and choose Open. After installation is complete, you'll have to restart again.
3) Now that IntelliType is installed, once again boot to the Recovery partition and this time in Terminal enter:
csrutil enable
4) SIP has now been re-enabled, so you have the extra protection SIP brings with it, and IntelliType is still installed and functioning.
5) IntelliType will not load automatically on a startup or restart because it fails to add a Login Item to your user account. You'll have to add it manually. Follow the instructions here:
https://discussions.apple.com/thread/5027397
Also, be aware that with SIP enabled, it's not at all unusual for IntelliType to suddenly stop loading on a startup or restart. Might work for a fews days, weeks, etc, and the OS randomly decides the kernel extension shouldn't be allowed to run. Then you have to go through the whole process again to get it working. The only sure way to avoid that is to disable SIP permanently.
If the only keys you really care about are Command and Option being in the correct Mac positions, you don't need IntelliType at all. Just open the System Preferences and click on Keyboard. Under the Keyboard tab, click Modifier Keys at the lower right. At the top, there'll be a choice for MS 4000 Keyboard (it's not there if IntelliType is installed). Then simply change Option to Command, Command to Option, and click OK.