4d images also work fine in Matlab (V2014b):

marker = ones(3,3,3,3)
mask = marker;
mask(2,2,2,2) = 0
im = imreconstruct(marker, mask)
% result: no error message, im == mask, class(im) == double

Here are some results from Matlab 2014b:

marker = true(3)
mask = logical([1 1 1; 1 0 1; 1 1 1])
im = imreconstruct(marker, mask)
% result: no error message, im == mask, class(im) == logical

marker = ones(3)
mask = [1 1 1; 1 0 1; 1 1 1]
im = imreconstruct(marker, mask)
% result: no error message, im == mask, class(im) == double

marker = ones(3,3,3)
mask = marker;
mask(2,2,2) = 0
im = imreconstruct(marker, mask)
% result: no error message, im == mask, class(im) == double

My conclusions are:

• There must have been a change in Matlab behavior between your Matlab version (what version is this?) and todays (R2014b and R2015a) version. Nowadays they DO the clipping if marker > mask, as their documentation says. (For logical inputs as well as class double inputs.)

• Yes, the Matlab version of imreconstruct does also accept 3D data. Despite their documentation saying differently.

I only needed to comment out the code that makes the check to get the results you wanted.  See https://bitbucket.org/carandraug/octave-image/commits/2c4e414f727c8edc87246172ba1821d04ae3791e

But I'm not sure it and need more testing if there's any assumption in the algorithm about it (I'd prefer to avoid having to actually modify the raw data -- although there's another step that already makes a copy so maybe it's not a big deal).

Note that the Matlab documentation also says that the image needs to be 2D which is not true. Testing in Matlab, I actually get the error about marker being higher than mask if I use non-logical:

>> imreconstruct (ones (3), [1 1 1; 1 0 1; 1 1 1])
??? Error using ==> imreconstructmex
MARKER pixels must be <= MASK pixels.

Error in ==> imreconstruct at 77
  im = imreconstructmex(marker,mask);

Can you test this in a more recent Matlab version?