Does merger control really affect market structure? Pretty much since 1976 (the passage of Hart-Scott-Rodino Act) US antitrust authorities have been reviewing mergers, challenging only 1.8 per cent of the total number of above-threshold notifications (IIRC I read it in a book by Bob Pitofsky).

What are the studies that control for changes in technology, capital availability and perhaps other factors and quantify the impact of merger control on economy-wide market structure/concentration measures?
Clifford Winston´s excellent book Government Failure versus Market Failure: 
Microeconomics Policy Research and Government Performance surveys the literature on the effects of government regulation generally and antitrust merger control specifically. He doesn't exactly answer your question on economy-wide structural effects, but largely concludes that merger control is rather ineffective. A small quote:


  Evidence from the finance literature indicates that mergers that were
  challenged by the DOJ and the FTC were in general not anticompetitive
  and would have been efficient had they been allowed to go through
  (Eckbo 1992). Mergers that were challenged or opposed by antitrust
  regulators but were consummated anyway have often resulted in gains
  for consumers (Schuman, Reitzes, and Rogers 1997; Morrison 1996).
  Finally, Crandall and Winston (2003) analyzed the effects of merger
  policy on price-cost margins and found that the antitrust authorities
  have primarily attacked mergers that would enhance efficiency, either
  by blocking them in court or allowing them to proceed only if the
  merger partners agreed to conditions that turned out to raise their
  costs.