stencil functions seem present on wrapper : https://github.com/BeWorld2018/SDL/blob/MorphOS/src/video/morphos/SDL_amigagl_wrapper.c#L1457

so i dont know if SDL2 is problem

i see that on SDL2 sources :
https://github.com/BeWorld2018/SDL/blob/MorphOS/src/video/morphos/SDL_amigaopengl.c#L104

Can you try to compile last SDL2 and test it (or i can send you my last library)