I took a small look at your repo and noticed a possible issue: while Gravis Ultrasound did linear interpolation of samples [1], on Amiga all sample replay was strictly non-interpolated [2] ... essentially on each display scanline the hardware would check the period down-counter and load the next sample if zero was reached.
Thanks for looking at the repo and for the links! Initially I just used non-interpolated output, but it was extremely noisy. I suspected the Amiga had some additional analog hardware which avoided this, so I just added some interpolation to make it sound better. But anyway, it's far from finished, if I have the time to pick it up again someday I could make it more accurate...