you would likely see more delay variation due to the trace lengths than the 0 ohm resistors. stuffing variations to make a product work differently are pretty common in products I've worked with in the past.
Just make sure the numbers associated with the two different BoMs are different so they know they are producing one product or the other. I vaguely recall we had a BoM part number with a variation on the end such as -1 or -2 and we could specify an order with either the -1 or -2 suffix. The variations had something similar to what you have a stuffing difference along with a part difference.