TMT at APO would never be built because it's not that good a site. TMT at Armazones would be no different other than the enclosure would be modified for the conditions. Yes it effects the performance and science case slightly but you don't redesign a telescope because of that.
Money is committed on the basis of guaranteed time not on the basis of performance. The money was even committed before the design was finalised. There is no agreement for example over which bodies will receiver dark time and good seeing, those scheduling decisions are far more important in performance.
The telescope is not that specialised.