It's not the same. I can open, process, or skim a directory containing a thousand files without much trouble or CPU activity. Having a thousand files worth of information in one file means I have to run through all that data at once. This has implications in data integrity as well if I'm making changes or worried about bitrot.

So, no, there's a difference. I'll also note that Daniel Bernstein of qmail & NaCl often used a filesystem how some use databases under the philosophy of "Why create new, complex functionality when you have well-tested code that gets the job done?"