In my opinion, the wood presentation case adds value mostly when the gun is in pristine condition. Then, the entire package (gun, case, tools, paperwork) is in the realm of what collectors look for, where such things are important, and a case is integral to overall value of the "set".
For many of us, in the "accumilator" category, depending on the condition of the gun, the case is not as important and that extra "window dressing" needlessly adds cost when the gun is in "shooter" grade and is less for show than using.
But there are also those that want the case regardless, and are willing to pay extra.
M28's are utility grade "service guns" and only came in the blue factory box, the M27's, M29's, M57's were common with the presentation cases. The cases are not numbered to the gun.
It used to be that if you're looking for a "plain Jane" shooter, the M-28 was the best value, because it was a no-frills, inexpensive version of the M-27 that performed every bit as well. But the M-28's prices have been driven up quite a bit by more people now realizing just how good they are and the resulting increase in demand. Used to be a good M-28 could be had in the sub $500 range... not anymore.
Hope that helps.