Two options are currently available for the manipulation of intra-zonal cells; specifically:
Setting a fixed value for all intra-zonal cells
Creating intra-zonal values based on the minimum of all other cells in a row.
More specifically option (2) has been created in order to set intra zonal costs/times/distances etc. equal to 0.5 times the minimum cost/time etc. to that destination from any origin (excluding those O-D cells which have zero cost). Otherwise skimming normally sets intra-zonal costs etc. to zero which may not be useful if there are positive intra-zonal trips.
In the case of matrices which have multiple levels and/or blocks then the definition of which cells are intra-zonals are based on the individual sub-matrices. For example, if a basic 10X10 matrix has 3 levels then element in column 1, row 11 is clearly the intra-zonal for zone 1 but in level 2.
N.B. The same definition of what is an intra-zonal is not necessarily universally applied within MX;, e.g., prior to version 11.6 it was not always used within the selection options (10.6.1).