"...as long as the modified software is itself available under open-source terms."I think the above is the important point with respect to national security. Why would anyone that cares about national security promote the idea of releasing all modifications back to the open source community?
Do you avoid buying padlocks from the popular commercial lines, because I could buy the same padlock, learn its flaws, and thereby gain illegal access to your property? No, having a market for padlocks increases the quality of all such padlocks, and reduces their price. What you don't do is tell me what you have padlocked, where, with what brand of lock, and what of value lies behind that lock. Obscurity as to the particulars of your situation helps you stay safe, even as you use widely distributed and publically available means to padlock it.