The ground cable fits better with the older version of Indivision AGA MK2. The new MK2cr version lacks one mounting hole and does not use the plastic stand-off any more (it now stands on the 20-pin connector), and the remaining mounting hole is indeed pretty far away from all motherboard screws, and mounting it on the shield or on one of the D-Sub screws at the back of the Amiga 1200 are the only options left.
If the shield is installed, the grounding cable can be left out. It is most important on tower conversions that use a plastic case, such as the Mikronik tower. Other tower conversions also leave out the shield, but since you're in a tower, you should have grounded screws nearby - plenty of options to choose from.
When the development unit failed CE pre-screening, I decided to play it safe on the final inspection day. Not only did I put all these 100R resistors into the "fast" lines as source termination, I also added the GND cable. The unit passed with flying colours, but the GND cable is on the official photo documentation, which is why I have to include it with every unit. I'm pretty sure that the source termination alone has brought down those nasty peaks in the spectrum, and the GND cable only did a minor improvement.
Since the GND cable is already fairly long, it probably does not help very much on EM emissions, but more on EM immunity: This is the second large verification where nasty EM is radiated into the Amiga, which either has to continue working, or self-recover from undesired operation. Here's where Kick3.0 and higher comes in handy: You don't have to click LMB any more to leave the Guru message, so it now counts as "recovered from undesired operation without user interaction" (ever wondered why this behaviour was introduced? Now you know why ;-)).
In essence, since the customer legally becomes the vendor of the complete system, it's up to the customer to decide whether the GND cable must be installed or not.