Regarding

> The only thing that bothered me is that gender affirming is in fact an amputation, because they gave their clitorises to science.

one of the linked articles reads

> Peters collected samples from one side of dorsal nerve tissue, a small amount of which is typically trimmed during gender-affirming phalloplasty procedures.

which suggests the situation was perhaps less bothersome than you thought. (It sounds like the outcome was identical from the perpsective of the transmasculine individuals getting surgery- the only difference was the choice to analyze medical waste).