tufsu1 has a point, regarding the Winn-Dixie store. $3 million doesn't stretch that far. However, it would be interesting to know the stage these plans are in when they come up before the DRC. From looking at many of the renderings posted in this article, it appears these projects are well into CDs when they are being presented. Something as simple as possibly laying out the new deli expansion area to potentially partially face the sidewalk/with outdoor cafe-style seating can be difficult to achieve when the plans are already drawn up and ready to go in for permitting.
In essence, the DRC's hands may be tied by evaluating projects too late in the design process. Imo, something that may help the situation would be having Architects/applicants bring their concepts in for review during the beginning of the Design Development stage, as well as the city being a little more strict with the zoning overlay. If people know they can't get away so easy with variances, from the beginning, they would be more inclined to design according to the zoning overlay's standards.