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Unless you lean heavily on the project tree, it's surprisingly not too different than a project, if you have reasonable tooling (search, LSP, ctags, etc)

My personal preference is certainly using a reasonable folder structure.

index.php is a bit of a meme at this point with his projects. It's not just one file anymore, but he does focus on radical simplicity with the tech.

I think he commented ITT and said he had an epiphany of sorts where he realized the tech doesn't matter.

People love debating the merits of one JS framework over another, debating back end languages/frameworks, etc. and in the end, for most solo SaaS none of that makes a difference in success as defined by MRR. I think, myself included, so many side-projects with the intent of revenue get lost in the SeaOfShinyThings™ and never find a port.