The reason to follow WP standard is for another DEV to pick it up later, or to transfer it without issue.
The problem is content. I could easily make a site from pages regardless of your plugins/themes if the database was set up in WP. But you are saving content differently so now I have to convert the data to WP tables, write rewrite rules and 301’s. That is a lot of overhead.
Why not do it all in WP to begin with? Your client might want to move, and you could help them, making yourself look like a champ.