I have a number of issues with this study. The first is that the primary purpose of the permit system was to improve the wilderness character and then the visitor experience. Safety is the 4th objective, but even then it is more specifically for the cables section, the actual permit required area, so that people can freely move up/down the cables if needed, say in a thunderstorm. Safety along the rest of the trail is obviously an added benefit, but not the primary one.
The other part is that the study is using SAR calls as a proxy for safety. That makes sense, but that assumes that all medical & safety issues have and do result in a SAR call or that the rate in which those incidents result in a SAR call has been constant. What the study is really tracking is the number of SAR calls in that area and more specifically the per capita SAR calls in that area per Half Dome hiker. There could be any number of other factors influencing the number of SAR calls that are not related to the number of needs for a SAR call. Some initial ideas would be the increased prevalence of cell phones, people carrying cell phones while hiking and increased cell coverage area. (The study goes back to 2005) There are likely more rangers patrolling the area, so more chances for a SAR. Other factors could be general increase in park visitation, general fitness of the population or something else that I can't think of right now.
Otherwise the study also included SAR's not related to the permit system like technical climbing accidents, illegal activity like base jumping, suicides and helicopter rescue because of a fire. The study area includes the section of the JMT from LYV to the Half Dome Trail junction where many incidents may not be related to Half Dome hikers.
Of course there could be an increase of incidents on the trail, due to 'summit fever' or because of implicit pressure to complete the hike on the permit date as permits are difficult to obtain or other factors, but this study has too many holes in it to determine that.
The line that best sums up the quality of this study to me is this line:
"Since the conclusion of this study period, YNP reduced by 100 the number of available daily permits. The rationale for this additional reduction was not provided."
This happened in 2012, and there is a document on the Yosemite webpage in the Half Dome Plan Information page explaining it and is clearly and prominently linked.