Looking at the appnote, I can't help but thinking somebody at Motorola messed up the oscillator design big time. The phase margin to make the oscillator work is probably incredibly thin. Also, the i.MX1 series is rather old. Why use such an old chip which is likely to become obsolete any day? I'd use a more modern SOC which likely has a better oscillator. Another option is to use an external oscillator instead of a crystal just to be sure.
Either way, in this case I'd try to adhere to the suggested layout to avoid having problems with the oscillator. Maybe put a ground plane on the bottom layer and stitch it together. I don't think EMC is a big problem as this processor is rather old and not very fast by modern day standards. A single 4 or 6 layer board is hard to get wrong bad enough to cause EMC problems from digital circuitry.