Synchronous FFT meaning DAC & ADC working off the same clock & the tones generated with correct crest factor & frequency intervals (I presume the free tools do this?)
Yes, but you need to do the work. It's the classic canned user friendly software aimed at a target audience vs. a full R&D tool. Much of the work in the scientific and academic community has been paid for by tax dollars and is free to the rest of us. Python with scipy and numpy add ons or Octave come to mind. Both will do just about any of this stuff.
EDIT - By synchronous here I mean the frequencies are exactly centered on FFT bins. DAC/ADC clock frequencies are also important and are preferably the same. I had a sound card (pretty well known one) that had a flawed 44,100 Hz clock and a 1kHz exact tone came out 1.006kHz (verified with an Aglient frequency standard) that no one ever noticed.