eGPU, a recently-reported soft GPGPU for FPGAs, has demonstrated very high clock frequencies (more than 750 MHz) and small footprint. This means that for the first time, commercial soft processors may be competitive for the kind of heavy numerical computations common in FPGA-based digital signal processing. In this paper we take a deep dive into the performance of the eGPU family on FFT computation, in order to quantify the performance gap between state-of-the-art soft processors and commercial IP cores specialized for this task. In the process, we propose two novel architectural features for the eGPU that improve the efficiency of the design by 50\% when executing the FFTs. The end-result is that our modified GPGPU takes only 3 times the performance-area product of a specialized IP core, yet as a programmable processor is able to execute arbitrary software-defined algorithms. Further comparison to Nvidia A100 GPGPUs demonstrates the superior efficiency of eGPU on FFTs of the size studied (256 to 4096-point).