Still playing around with this today, and curious to see what others are coming up with as results. I've made a change in the script already, and it seems to be getting a bit more accurate on large file counts. So far, the comparisons are pretty close. Here's what I'm getting for file counts from various sources on two of my domains.
Domain 1:
My PHP Script: 6606 Files
FTP Login Msg: 1367 Files <--

gotta be a 000webhost glitch
FTP DL Queue: 6612 Files
Domain 2:
My PHP script: 3141 Files
FTP Login Msg: 3137 Files
FTP DL Queue: 3145 Files