What I see is that TRFF=2 and DECON=2 either (1) fits a little better than TRFF=1, or (2) fits a lot worse. Case (2) is fairly rare, but you will find some examples below. When TRFF=2 fails, it does so spectacularly. However, this happens when the pulse is wide, and the TRFF=1 peaks are rejected for being too wide. Based on this comparison, it is hard to say conclusively which is better.
Looking at the spectra from the comparison above, we wondered if the constraints on the two sigma parameters are messing up the TRFF=2/DECON=2 fits.
By default, and in the comparison above, the constraints are sig1_hi = 3, sig2_hi=5, as provided in the HIT_SW table.
In this, comparison, we look only at TRFF=1/DECON=1 vs TRFF=2/DECON=2, but we have loosened the cuts to sig1_hi = 6, sig2_hi = 10.
From this comparison, it is pretty clear that TRFF=2/DECON=2 is better.
Also in this comparison, I have "enriched" the spectrum sample so we can look at some spectra with many peaks. Unfortunately, many of our "multiple-peak" spectra result from poor pedestal subtraction, to which the two deconvoluters react differently (TRFF=2/DECON=2 seems more robust to this).