It is annoying. But I don't think it's dishonest. At least one knows which leg of the route the upgrade will automatically clear.
I see it often on my favorite AA route (SFO-LAX-HKG). SFO-LAX, get upgraded to F with the SWU. Waitlist for LAX-HKG. Why not just call EXP CS and ask they to apply the SWU for the BOS-LAX leg only.