"As I see it, the only solution is to input whatever number in the 1099-B fields to force a net STCG total that matches the actual STCG; in this case, about $3M.  That way, the proper gain amount flows to other schedules."

That's what I'd do.

"The question is -- if the total sales and total basis don't match up between Schedule D and the detailed PDF, will that cause a problem.  Perhaps I could attach a statement explaining the field limitation issues, or would that further confuse the issue?"

I'd probably do this, too, but explanations usually don't get read. You can probably expect a matching notice to which you'd reply with the same explanation and can point out it was attached to the return.