I am using the multiple CSS entries and it is very nice.
I am compiling multiples themes and their input file are always app.css but in different folders.
I think it could be great to use the folder of the input in the output file :
https://github.com/SymfonyCasts/tailwind-bundle/blob/main/src/TailwindBuilder.php#L113
Maybe with a hash or using the %kernel.project_dir%/folder/to/the/file/app.css to folder-to-the-file-app.css
Or give the outpile file in the configuration for each entry