The difference is more money, up to 75%. Your retirement pay is calculated in most cases by multiplying the award times your retirement base pay. So, each increase gets you more money, up to 80% (which, because the law limits retired pay to 75% of retired base pay, is the highest you can get....but yields 75% only).
Now, it gets more complicated because for the majority of Servicemembers with less than 20 years of service, there is an offset from VA compensation each dollar gained from the DoD. So, for some, they will do fine at the VA and there is no benefit. However, if you qualify for CRDP or CRSC, you may double dip (in whole or in part) and thus it may be very beneficial to have a higher DoD rating.
So, why the big deal for fighting for DoD retirement? First off, the healthcare benefits for you and your family. A recent Government Accountability Office report pegged the value of this benefit after age 60 as approximately $175,000. So, the younger you are, the value of this benefit shoots up dramatically.
The other important reason to fight for a high rating from the DoD is that while most Veterans eventually end up with a higher rating than their DoD rating, this does not always happen quickly. It can take years to sort out a VA claim (and it is sometimes the case that the higher rating is a result of a condition deteriorating over time). The DoD rating pays out immediately, so it can be an important source of income while you transition (and in some cases appeal the VA rating decision). Also, remember, with the exception of TDRL, DoD ratings are permanent. So, even if you get better, you keep the benefit. The VA will reduce awards if you recover.
Theoretically (and excepting the DoD/VA Pilot program) the two systems are not bound by each others decisions. But, anecdotally, I believe that a higher rating in one system will tend to help a rating in the other system. Now, this would be very hard to tease out if there is a cause and effect relationship or it is just because the seriously injured deserve high ratings from both systems. My opinion is that it is best to have a rating as high as possible from both systems.