That's funny, I started noticing a similar sound with nearly identical conditions to those you just described. I didn't post yet because I haven't had a chance to look into it as much as you have.
I began noticing distinctly when I start the car to head home from work. I can still pick out the sound when I pack at home, but its not as distinct as when I start it up-- maybe because I've adjusted louder wind/engine/road noise on my drive home. This sound appears to also vary with rpm in terms of the frequency of knocking, but it doesn't get louder. As with 31Hertz, the car also drives fine. Initially I thought it may just be valve tap as both a mechanic who did the pre purchase inspection and a friend of mine who's got two e28s picked up and mentioned that.
AFAIK the clutch hasn't bene changed since the PO swapped in a manual 6spd about 90k-100k ago.
Sorry I can't help more, but I'm interested in any ideas you guys have.