The additional risk arises if the primary tank has only one main reg and no secondary reg. Most people using a pony install only a single reg on the main tank. I instead always use two (complete, two first stages, two second stages, on two independent valves - and my main 15-liters steel tank has also the reserve).If a diver breathes off a pony to extend a dive, relying on the reserve in the main tank to get to the surface and then experiences a primary regulator problem or blown hose, they are in the same exact situation as the typical diver who uses only one tank.
In other words, extending a dive using a pony bottle, while leaving the typical reserve in the main tank does not create any additional risk, while giving the benefit of having redundant air during most of the dive (prior to extending it with the gas in the smaller tank).
So, when using a pony (not always, in my case, but only for "heavy tasks"), I end up with THREE complete and fully independent regs, each with its own valve.
At that point, however you use your pony, it does never diminish safety compared to not having it.
But if the pony means moving the secondary reg from the main tank to the small bottle, then you could have a problem: if the primary reg fails, you have no backup on the main tank...