Sorry but this can not really be done. Like you already said, some hacks also change the database. I can not give a general answer because some hacks might add to existing tables, and others would create their own. So not easy to give a general answer on how to duplicate that data.
With 3.5 (as long as you stick to plugins/extensions) installing hacks is not a lot of work, so you might want to think twice before going this way.
To make just 1 version of the scripts you could rename your config.php to config_domain.php. Then create a new config.php, and in this new file load the correct config_domain.php based on the domain.
Styles are not that difficult, just create/edit them on 1 board, export the XML, then import into the other boards.
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