I have done some tests regarding alpha, thinSSS and backface materials.
The biggest slowdown clearly comes with the alpha channel, especially when there is a direct light source like sun or a high contrast HDRI.
The backside material seems only to add noticeable to the rendertime in combination with clip maps AND thinSSS for physical sky, but with HDRI also without clip map.
(It looks like a contrasty HDRI produces significantly more noise than phys sky - not sure if there is a way to optimize the HDRI to decrease the noise without loosing the contrast. )
Leaf geometry (384 polys / almost 50% clipped)
The leaf material has one layer with 2 BSDFs (diffuse/reflection) for the tests without ThinSSS. ThinSSS adds a third BSDF.
Scene: 10x1.5M polys instanced.
Sky with sun (sl10)

full size
http://abload.de/img/sky_sunj3fqi.jpg
Sky only (sl10)

full size
http://abload.de/img/sky6je20.jpg
HDRI (sl10)

full size
http://abload.de/img/hdri6fd3b.jpg
Comparing the amount of clipped geometry to rendertime (standard diffuse material)
Rendertime seems to increase almost linearly with the size of the clipped area with ~15% more render time per 10% clipped geometry.
The subdivision of the textured surface seems to add maybe logarithmically - but less with increased complexity.
(without intersecting faces)

full size
http://abload.de/img/alphatest_0-10-25-50pxuiyv.jpg
edit:
Finally i did some tests comparing instances to mxs-references (backface material + ThinSSS + alpha) and it seems that mxs-references are a bit faster than instances (2-3%)
I don't know if this is scene dependent and 2-3% is not such a big difference, but at least it is not slower - that was what i expected.
...if the mxs-ref render doesn't crash because of the backface material - there seems to be a bug.
And another thing i noticed was the brighter color of the instances compared to the original tree (left tree first row). There must be something wrong with instanced clipped thinSSS-backface materials. The mxs-ref version does not show this problem.
