The ParamChem charge assignment is described in K. Vanommeslaeghe, E. P. Raman, A. D. MacKerell Jr., J. Chem. Inf. Model. 2012, 52, 3155-3168.
The two charge sets in the main file are very close; I don't expect significant differences in the properties. Each of the fluorines is 0.01 less negative in TFE, but the overall CF3 group is 0.01 more negative (the slightly larger difference for the C is of little consequence because that atom is buried). The sign of the difference for the overall CF3 group doesn't look very physical, but again, the magnitude is insignificant. The person who did this was probably fine-tuning water interaction energies within a very small margin. If it would be me doing it now, I would keep them the same for the sake of transferability and to avoid overfitting, but at that time (1999), CGenFF wasn't conceived yet and people were less concerned about transferability.
Moving on to the subject of your molecule, this is a case where manual charge assignment would be unambiguous, so you don't need to use the ParamChem charges (though it wouldn't be a huge mistake to do so). For the purpose of transferring charges manually, both charge sets in the main file are probably equally good. TFE has an oxygen in the same position as your C(alpha), and the oxygen is probably a stronger electron withdrawing group, but TFET has no electron withdrawing group at all. At the end of the day, since there is less potential for secondary interactions in the TFET charge optimization, and that molecule was studied extensively in the paper you're citing, I would agree with you in feeling slightly more comfortable transferring from TFET, but yet again, it matters little.