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As you discovered, the "Replace Thing Id" is *always* applied. It's purpose is for when you want to completely replace a built-in thing with your own customized behaviors. You can't do it conditionally.
In order to have the behavior be conditional on a source, you'll need to define two things. First, you need to define the new feat that will be used in Alice's game, and then make it dependent on the source tag, just like you've already done. But do *not* have this new feat replace the standard one.
The second step is to create a copy of the standard feat for Bob's game. This one should be designated to replace the standard feat using the "Replace Thing Id". The only change you need to make to this thing is to have it be conditional on the source *not* being selected. Every source defines a global tag that you can test against, and the standard "Sources" mechanism provides a simplified way of checking for the selection of a source, but you need to check that a source is *not* present, so you can't use the simplified mechanism. This is achieved by adding a ContainerReq to the new thing via the button on the right within the Editor. For the ContainerReq, select the phase "Testing Global Tags". For the tag expression, enter "!source.MySource", where "MySource" is the id of the new source you've defined for Alice's game. Then save the thing.
At this point, you have two distinct things. One of them is only used when the source for Alice's game is enabled and the other is used whenever the source is *not* selected.
Another simple way to handle things like this is to clone the complete set of data files for the game system. You can go to the Tools menu and select the "Duplicate Game System" option. This will create a copy of the data files that you can customize independently of the standard data files. If Alice's game has lots of customizations, you can copy the Pathfinder files as "Alice's Game". Then you can add the customized things specific to her game only to that set of data files. When you create a character for Alice's game, use that set of data files. Otherwise, use the standard set of data files.
Hope this helps....
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