I think your two-step solution is the correct one! Ideally this would not need to be the case, but Cutadapt can tend to need to be told exactly what to do, and in your case it seems to have to be told in two separate steps. You can see the same thing occurring in this recent post and the referenced, older post.
Unfortunately we are not the developers of Cutadapt and q2-cutadapt is just a wrapper. At this point we are going to recommend exactly what you did!