Any method, which hides the function, make it unaccessible - according to the definition of "hiding".
Another strategy is to collect the init files with individual names in a separate folder:
MFiles\inits\init_MyToolboxA.m
MFiles\inits\init_MyToolboxB.m
MFiles\MyToolboxA\
MFiles\MyToolboxB\
Now only MFiles\inits\ is stored persistently in the path and Running init_MyToolboxA adds the folders of the toolbox "A" and performs any individual initializations.
On the other hand having an init.m in each folder is not too bad. E.g. Matlab stores a "Contents.m" in each folder also without causing troubles or confusions. You find multiple "prefspanel.m" also.
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