I see both sides of it, but at the same time, if companies like VKB, Virpil, and TM are making these "modular" HOTAS systems, it would be nice to offer the consumer the options of assembling their own units, based on personal preference and play style.  At the same time, I understand their concerns about firmware.  Further, from a branding standpoint, I can see why they would only want to sell THEIR sticks with THEIR base.  Don't exactly want to market for your competitors, do you?   
All that being said, I wish I could buy the base standalone as well...