I just noticed this today, although I haven't tested applying quickness before true nature. But yes I thought this as bug as well. If True Nature is applied it should add 3 seconds on to any boons. My quickness is at 3.5 seconds baseline, with or without True nature active, quickness applied is always at 3.5 seconds.
After testing with quickness already applied I can confirm it doesn't add any more time to the boon.