Overview appears to use its own effect (a zoom) to change desktops which does not conform to what is set under the effects settings. E.g. I have mine set to slide so when switching in various ways (e.g. when click an entry on the task manager for a window on a different desktop), the slide animation is used. Since desktops can be arranged in a user-configurable grid, the current overview effect does not help the user figure out which desktop they've moved to in the grid space. This is why I prefer the slide animation which lets you know where you've moved to.
The effect you're talking about is used when switching from one desktop to another. However when switching desktops from the Overview effect, you're starting in the Overview effect, not in a virtual desktop. So an animated effect that switches from one desktop to another one does not apply and cannot be used. That's why the Overview effect uses a "zoom out" style animation. To be able to use it, we would have to first close the Overview effect, and then play your default desktop switching animation. If it did this, would you be okay with the fact that it would necessarily make desktop switching slower because it would need to play two animations (leave overview" and "switch virtual desktop") rather than one?
Good point. However, when you click on a thumbnail, overview could exist without an animation followed immediately by the user-defined desktop switching animation. Is that any better though?
Since it opens with an animation, I think it would be weird for it to close without one.
I've also found this jarring. I think it's important for visual consistency to use the animation that is normally used for switching desktops. This matters even more when mixing a desktop arrangement that is spatially presented during switching -- as with sliding desktops when arranged as a grid. ..and once someone does Desktop Cube in the new framework, it'll be helpful there, too. But consistency matters a lot, and having a consistent animation makes the association on a visceral level that 'desktop switching' is happening, and happening normally. The animations can both be done, and there are a number of reasonable ways to do that -- playing both chained together as an InOutCubic (if that's possible) would make sense. But also, if mixing is possible, that could be done -- the windows return to their normal positions as that desktop slides away. Even playing one right after the other (as an option) would be ok. In any case, I suppose you could consider this another vote in favor of addressing this issue.