I improved it in the last update for FactorioHD:Production, but it isn't perfect, those black "lines" in the pipe sprite actually exist in vanilla https://prnt.sc/vfo7kz , when they're upscaled it makes those lines more pronounced.
Fixing it is going to require manual work on my side, so it's "good enough" for now, but I'll try to improve it when I have the some time.