Customise markup for publishing

I have adopted a habit of using source code comments with a lot of 'bang':

%==========================================================================
% Create Triplet Indices
%==========================================================================

Imho, they add a lot of structure to my code. However, this markup conflicts with the publish function of Matlab, which forces me to use

%% Create Triplet Indices

to achieve the same section title in a published document.

Is there a way to customise e.g. the section title markup? Alternatively, would it be possible to strip certain markup before publishing using e.g. regex?

As an example, i could live with

%%==========================================================================
%% Create Triplet Indices
%%==========================================================================

and strip the lines.

Cheers,

Johannes