The T-46A's design was heavily influenced by the SAAB-105. Fairchild and SAAB had entered into a partnership to build the SAAB Fairchild SF340 turboprop commuter aircraft and collaborated on the T-46A. The SAAB 105's lines are readily apparent in the T-46A's layout. The H-tail was probably used over the SAAB's T-tail to increase spin recovery and effective control at high angels-of-attack. The winglets, I'm assuming, was to increase fuel economy at altitude as the Eaglet was supposed to be pressurized and cruise up to 41,000ft.
The T-46A was cited by the USAF as having a number of deficiencies. The largest problem was the amount of drag that it produced. I can imagine that the drag issue came up during wind tunnel tests and as a means to reduce drag and increase performance the winglets could have been considered. Ultimately, after the design was frozen FRC had chosen the Garrett F109 engines with a thrust of 1,330 lb st each. The USAF wanted FRC to use the TFE76 demonstration engine of 1,500 lb st. due to concerns over potential weight increases, but FRC decided a use a smaller engine in development with Garrett.
The GAO highlighted these performance deficits:
1. High drag
2. Lack of adequate stall warning
3. Roll trim issues
4. Speed brake buffet
5. Airframe weight increases
Program mismanagement was also cited as a severe problem in the T-46A program at FRC, with slipped delivery dates and substantial cost overruns.