It does leave the app open to beginners tinkering with the external plain text files.
That's funny. I externalized scripts (mostly Excel) because the users had to have write access in order to allow modification of the Excel data, but because the script was external it could reside in a read-only folder. Also, the Excel files were generational (a new one for each day) and having the code in each file would have been a nightmare managing code changes. With an external script I only ever had to modify one file.
One other advantage was that my scripts had to determine whether or not a given date fell within daylight saving time or not (transition days were especially painful because of the skipping or duplication of the transition hour). I had dozens of scripts that relied on this logic. When Bush (younger) changed the start/stop dates I only had to modify the DST logic class code in one place (the library that was included in all the other scripts). Other programmers had to modify/test code changes in dozens of applications.
It also helps to organise your code - having a html page to throw all your various scripts into is horrible - you can place unrelated scripts into separate files.
You can also minify and gzip external files (you can also minify in-page scripts, but it sort of defeats the purpose).