It's not overclocking, like was discovered on the S4, which is technically worse. I'll try to explain it. During normal operation the CPU is constantly changing speed based on demand. That's great for power management. It means that the CPU can idle most of the time, and ramp up speed when you're doing stuff. If you were to look at a graph of CPU speed doing anything (and I mean anything, since nothing will ever peg the CPU to max speed continuously) it'll have peaks and valleys. Kind of like a heart monitor. It's very dynamic and is almost constantly changing, especially with the current crop of quad-core CPU's. Each core will also be able to operate dynamically, which helps with power draw and thermal management. That last point is something I will touch on further down.
The goal of a CPU is to get work done as fast as possible and then get back down to the idle state, where it's drawing the least amount of power. "Race to idle" is a term you may have heard before, and that's what it's referencing. You open an app and the CPU speed spikes, then goes back down. It did what it needed to do and went back to an idle state (or the slowest it could go while still giving good performance for what you're doing). So we've established that CPU speed is determined by the demands that you're putting on your device at that specific time. There's one other factor, though, and that's thermal management.
As you know, CPU and GPU's generate a decent amount of heat doing there job, especially when being pushed very hard. Games and benchmarks are apps that would stress both components. Manufacturer's have targets for thermals, and a max temp and time that temp can be maintained. Once that point is reached it will "throttle" the CPU/GPU, which basically means it will slow them down. That's for longevity and is something that's very common across different sectors. If you did any reading on the S4 Pro in the Nexus 4 specifically, you'll know that it was thermally limited when running benchmarks. LG/Google let the chip do all the management and didn't smooth performance out. Other manufacturer's are more conservative, and will establish limits that will give more consistent performance. Odds are that they know that most users would rather have a consistent experience over spurts of faster performance.
Based on what we know is going on then, OEM's have introduced a level of thermal and power management not available to any other app. While during normal operation a CPU/GPU will race to idle, when running a benchmark the speed is set to max the entire time. This prevents the CPU from powering down, which helps performance because it then doesn't have to speed back up. Over time, those milliseconds add up to lower benchmark scores. But what about the thermals? You can't just keep the speed at max and also keep thermals in check, right? They thought of that too, and have also changed the thermal thresholds (most likely) for this particular level of performance.
So no, they aren't overclocking. What they're doing, and this isn't just Samsung, is introducing a performance tier that's only available to the whitelisted apps. That brand new game that you just picked up that has amazing graphics will never see the type of performance that the benchmarks are seeing, because they aren't on the whitelist. The CPU/GPU will operate dynamically just like they would for another other app, and would only see max speed across all four cores on rare occasion.
Hopefully that all makes sense.