From an empirical point of view, I would say YES. Here is my reasoning:
A mountain bike typically has a more "laid back" geometry, which allows the rider to transfer more weight towards the rear tire. This allows to apply greater force to the brakes without going over the bars because:
The rear tire is effective for braking only until weight transfer lifts it and it starts skidding. If your bike geometry puts more weight in the rear tire (proportionally) than another bike, then you bike can be stopped in a shorter distance, for the same speed, surface, (bike+rider) weight, etc. using the rear brake.
The front wheel, is responsible for greater part of the braking action, but then again, if you have proportionally more weight towards the rear, you can apply greater force to the wheel. There is a limit for this though, since putting too little weight on the front tire makes it easier to skid it and loose control.
So, just by changing bike geometry, and assuming normal rider positioning (i.e. not getting out of the saddle towards the rear), the MTB rider can apply greater braking force. Add the psychological factor of feeling that you are less prone to flip over. With this alone, I would argue that an MTB is capable of coming to a stop in a shorter distance, but there is more.
A typical XC mountain bike is heavier than a road bike, so, both being a the same speed, the MTB has more kinetic energy, so to come to a stop it must get rid of a greater amount of energy. But since the MTB is already heavier then there is no problem installing slightly heavier brake systems. Let´s assume then that all that extra weight (in brakes) is exclusively to yield more braking power.
Another aspect is the use mode that MTB brakes receive. For example for DH riding, most of the braking is sharp, hard braking, on planned parts of the course, to the point that intentionally locking the rear wheel to skid it and make a sharp turn is a somewhat common technique. In XC the use is less dramatic, but the general idea is that Mountain bikes, for different disciplines usually have to negotiate technical descents, where it frequently will be necessary to reduce speed as fast as possible.
Road riding on the other hand, needs smooth speed control. I'm not saying that there aren't emergency stops, but they should be rare, and considering that road bikes are built to be lighter, on every part of them where you can shed weight, you should, thus designing an overly capable brake system, at expense of weight is definitely off the table.
From this, I naturally conclude that road brakes offer some minimal braking performance, sacrificing it for the sake of weight savings (And aerodynamic performance).
Putting it all together seems reasonable to think it is easier to stop while riding an MTB than a Road Bike, but to answer the original question, it's not that road brakes are underpowered, MTB brakes are overpowered (when used in the same condition as road ones)*.
From the few times that I have ridden road bikes, I agree that using the levers from the drops yields more braking power and control than riding on the hoods, but no matter if the brakes where top-line or 30 year old Dia Compe, they all felt "spongy" compared to the "solid" feel of a freshly installed v-brake. This "sponginess" I think cannot be other thing than material flexing in several parts or the system. If part of my effort is going towards flexing parts of the bike, that means less braking force.
*I would love to hear from cyclocross riders what type of brakes they use and what kind of descents they travel, I being partly DH rider and used to 203mm rotor disk brakes, get the chills just thinking of descending with drop bars and road brakes...