File exported via ZipExporter should be the same as the original file imported via createFromZipFile(). Some our internal tests are basing on this rule. If for some case they would not be, then it would be a bug.
I would say this highly depend on how the original Zip was created.
Which compression level was used?
Were empty directories stored?
While it maintain the same 'Files', are they exported in the same order as in the original?
Right, sorry, I've forgotten about those things, and our tests uses export as file rather than as input stream. From shrinkwrap side it uses currently deflate compression by default. Probably the best choice for you would be to test this in practice with your apks.