Hello @aryanrajseo
Thank you for reaching out and I am happy to help!
You are correct when you say that the W3 Total Cache Auto minify option when set to combine only does not combine all the files into a single file.
In order for the website to perform correctly without any breakings and because of the fact that the file location is different in the HTML, and that there are some dependent files, W3TC auto minify creates more than just one or two files.
You can however, use manual Minify and add the files in correct order and dependency. This will crate a single file (or two files depending on the settings)
Please note that the W3TC minify is much more complex as a setting and offers a lot of options. As an example, deferring a single file in which all of the JS files are added would cause the website to completely break.
I hope this answers your question.
Thanks!