What is the best way to organize template parts?

Question

Looking at the following source codes

you are going to have issues, more with your custom headers and footers. I do not know what portfolio is and how it will be used, so I cannot answers on that specific subject

get_footer() and get_header() does not allow for custom headers and footers to be loaded from a subfolder. Looking at the source codes, the only valid file names are as follow

For headers, it will be header-{$name}.php and header.php
For footers, it will be footer-{$name}.php and footer.php

There are no filters to adjust this behavior in get_footer() and get_header(). There is a hackish method that you can use here though. For this to work, you will need to name your folders as follow

For headers, you will need to name your folder header-{whatever}, where {whatever} can be anything you like
For footers, you will need to name your folder footer-{whatever}, where {whatever} can be anything you like

(Note: Using anything else than header and footer as prefix in the folder name will not work). You can then call your custom footers and headers in the following manner

get_header( 'whatever/header-centered' );

which create a filename like header-whatever/header-centered.php

As for template parts, I cannot see any issues right of the back. All you need to remember is to add the subfolder name as part of $slug

Instead of

get_template_part( 'content', 'single' );

you will need to do the following if your subfolder is called content

get_template_part( 'content/content', 'single' );