Alexandru Preoteasa

A layout gallery is just a file on disk containing any number of assets you add to it.
That one there happens to be the "example" file Houdini ships with. That one is read-only, it's only meant for you to have something to play with. (see the text there: Read Only Source: C:/PROGRA~1/...)
If you want to put your own assets in, you need to create a new gallery. Click the cogwheel right next to that text and when the menu pops up, click Create New Asset Database File..., then select save that .db file somewhere on disk.

File mode is just a shortcut for a File SOP. It expects something you'd load with that, like a bgeo.
Component Builder is a way of taking non-USD geometry and "packing" it into an USD asset (together with materials, variants, etc).

Using the first input of the foreach instead of the second makes the original geometry be used also as an input stage. That means the layer resulting after the foreach doesn’t contain just the “over” with the modified geo, but also the original layer.
While this is a totally valid approach, we usually like to keep things separate because it gives you the flexibility in the final stage to load/unload layer at will.

Usually these things happen in different Houdini projects handled by different departments. You would have the initial static asset published by the lookdev department, the animation would read these assets but only write inside their own usd file the changes they bring to the asset. Finally, when it comes to lighting for instance, the artist can start working with the static assets, even if the animation is not there yet, and load it in later at his own convenience.