We’ve been talking to Alarm.com and Liftmaster this morning about your issue and it sounds like you’re on the right track. The Liftmaster 888LM Compatibility Guide appears to list the 1246R (DS) as compatible but it also says “MOST with an orange/red learn button with gray antenna wire.” are compatible while “ALL with a purple learn button with purple antenna wire.”
Liftmaster says if it doesn’t work then you need to replace the circuit board with a 41A5021-1G to make it work. That’s what it sounds like you’re already doing. Are they charging you for the replacement board or just sending it?
Alarm.com is looking into this further but one person did ask that you try resetting the gateway to factory defaults to make sure it isn’t a stale data problem. If you would like to try that, here are the instructions:
Factory reset the Internet Gateway:
If you must force a full factory reset (a non-recoverable data
destruction “hard” reset) to the internet gateway, disconnect
power to the internet gateway and while powered off, use a thin
tool, such as paper clip or a toothpick, to press and hold pressed
the internet gateway’s reset button. While continuing to hold the
reset button pressed, connect power to the internet gateway.
Continue to hold the reset button pressed for 10–20 seconds
until the gateway’s Yellow light blinks, then immediately release
the reset button.
Finally, if all else fails you could return the 888LM/828LM and use a MyQ Garage (821LM) universal retrofit instead.