Alternate Layouts is designed to work with a completed original layout. When you now want to create alternates, such as different size ad mats, different tablet orientations, etc., you set up your Liquid Layout rules and start creating alternates. In itself, this is terrifically useful and can get you 80% of the way there, or better, with very little time spent compared to doing it all with copy/paste.
It isn't a simultaneous editing feature, and if you think through how Liquid Layout rules work you will see that it can't be. There is no way to establish a custom LL rule for an object that you haven't created yet.
It's not all a loss, though. Alternate Layouts actually creates linked objects in the alternates, similar to external file links. All the objects in the alternates are linked to their originals, so that if you change the original you will see the equivalent objects in the child layouts go out of date. This is another reason why you would want to complete the first layout before creating alternates: subsequent edits and updates will propagate through all the rest.
All of your master pages get named children that correspond to the name of your alternate layout(s), but they are NOT "based on" the originals, they are copies.
Adding a new object to an original document doesn't automagically add the same object to the various alternates, whether on regular or master pages.
You might consider these to be limitations of the feature, but take a broader look: I don't want a piece of software making automated layout decisions behind my back. Let it get me 80% of the way, when I create the alternate, but after that, I want the software to leave things alone other than to alert me when an linked object needs to be updated.
The best practice is to complete the initial layout (even if it will be subject to minor revisions or copy changes later) before setting up the alternate(s). This plays to the the way Alternate Layouts was intended to be used.