Yes, I have run into this as well - you are still subject to the same quantity rules as the Hours Accounting / Process Hours Accounting sessions. The standard session has this problem, so you will too.
The problem as you noted is that during Process Hours Accounting, basically, does not answer 'yes' to the question 'Automatically complete quantities on previous operations' (roughly) that you are given if you try and do the same thing in Report Operations Complete.
The only solution I have thought of, and I have not yet implemented this, is that when you have reported quantities complete, run that through to Report Operations Complete session instead of through the Hours Accounting. That one nicely allows you to enter 'yes' to that question. Down Side: You would not see the quantities in Hours Accounting, like they may be used to, but the labor would be reported properly and the quantities would be reported properly, so ... seems like it would work to me. It would most likely be a major coding change.
Edited: I just saw Darren's post. The count points will effect both Hours Accounting and Rpt. Op Complete quantity reporting rules, but the Process Hours Accounting problem goes even beyond that