Its actually not set to TDC, you want the sensor set about 60-70 degrees before top dead center. The EFI system has to fire the spark, and so when your timing is advanced by, say, 40 degrees, the EFI system needs to fire it there. So, it needs to have the crank sensor set up well before the point of maximum advance. I think FAST recommends 60-70 degrees in most cases.
So, for the sake of an example, let's say that you have the crank sensor at 70 degrees BTDC, and your idle timing is 16 degrees BTDC. When the EFI box sees the pulse from the crank sensor, it will wait 54 more degrees and then fire the #1 plug, so that it fires at 16 degrees BTDC.
Also, after you have the engine up and running, you can adjust the crank trigger point in the software (at least on the FAST XFI box you can). So, let's say that you have the crank sensor positioned at what you think is 70 degrees. You put that 70 degrees into the software, then fire the engine, and after it warms up and is idling the timing map says your timing is 16 degrees BTDC. But when you put the timing light on the engine, it says 20 degrees BTDC. What that means is that your crank sensor is not actually at 70 degrees, it is at 74 degrees. So, the EFI box is reading the crank sensor, and after it sees the pulse it waits 54 degrees and then fires number one. Since the crank sensor is actually at 74 degrees, 54 degrees later is 20 degrees BTDC, so that is what your timing light is reading.
To correct this you would add four degrees to the crank sensor position in the software. So, change the crank trigger point in the software from 70 degrees to 74 degrees. Since the timing map in the EFI software wants to fire the #1 plug at 16 degrees BTDC, it will now wait 58 degrees after the crank trigger pulse to fire #1, not 54 degrees. So, after making the software change you can put the timing light on the engine and you will see 16 degrees with the timing light. Now, you have the EFI box synced up with what the engine is actually doing, and all your timing measurements shown in the EFI software will be correct.