1- For the milking room, it can be done at the construction room once the chapter 1 of Daemonheim has been completed.
2- Yes, you can transfer your save to the patreon version. All you have to do is reinstall the game from the patreon link. The game will overwrite the files with the new one but your save won't be affected. The only thing you cannot do for now is transfer the save from the Hero tier on patreon (that is currently only for PC)
3- For the bottles, assign servants to the worker slots in the milking. Then, after every battle (or using the bed) bottles will be available for collection.