There is no impact on the loop in the current iteration. Gutenberg created content is just stored as HTML inside the post_content column of the database, and output with the_content(). Same as before.
As for site-customisation, you said it: No-one knows precisely at this point.
There are no technical details on how site-customisation will work exactly, or how developers will interact with it, at this stage. That’s the next phase of the project, so once the editor is merged, keep following the project to learn how it will be implemented, and possibly even influence its development.
Mel Choyce gave a talk in February which showed some early ideas for how customisation might work from the user perspective, but all we know technically at this stage is that the sorts of elements that will be used will be Gutenberg blocks.