The two arrangements produce different results, different overall sounds. Having stereo oscillators within an otherwise mono sound is quite different in effect to two different layers or units, even if these two are identical. I've many times compared the effect of the Poly Evolver Keyboard's stereo oscillators with a paired Prophet '08 Keyboard and Module. The two are definitely not the same, so I would still prefer the PEK's set up.
Seen from a technical point of view, the Desktop Evolver is a two-voice synth... the engine just run them as a "single voice" ... it's two voices with each an analog and digital oscillator..... with the added ability to pan them..... seen from this technical point of view, there should be absolutely no difference to a P12 which has two voices panned left/right using the same parameter setup.
It's a bit hard to conclude it by comparing it to a P08, as this machine is different in a lot of ways, so it WILL sound different... one major difference is that the Evolver has digital oscillators, and several other digital parts in the signal chain which may lead to a different sound...
If we imagine that the Evolver instead of the stereo configuration it has, had been made like the P12, where each voice is only monaural (1analog, 1 digital oscillator), and had each their own set of parameters, and the ability to use two layers with panning, then I'm 100 certain, it would sound exactly like an Evolver with a hardwired stereo configuration.
In theory, what gives this stereo config it's special sound is the fact that the oscillators are free running, and out of phase with each other... the same is true in the Layer A/B approach... I really do not see any other advantage to hooking two synths up together for L/R than that you have double the polyphony (which could definitely be a great advantage)...
If you use only one output from a P08 for the Left channel, and one for the Right, you might get some difference though, if you use the one output that sums to mono... could this be why you hear something different? ... if the two P08's stereo outputs are summed to mono, and the preset in use use both layers with panning for a stereo effect, then I'll admit that it will sound VERY much different... but in that case you are not using only two voices, but rather four.... two summed to mono on the left, and two summed to mono on the right.