The only way I can think around this would be to include all PHP files in a namespace's directory in your spl-autoload-register method. Your autoload method would only be run once, but it would potentially load a lot more than you had anticipated and/or needed.
I believe it's good practice to only have 1 class per file and have the filename share the name of the class. Yes you have more files, but it simplifies refactoring and makes your file structure easier for other developers to work with.