Garret,

For the Bin/Lib parts, that's just your normal DataFlex runtime parts. There's good reasons to keep a runtime apart from your applications as otherwise you would have to put a runtime in each Program's folder.

You've had the "lucky" fortune to bump into modsecurity restrictions with the IIRC OWASP ruleset configured and that really was the problem.
If you had installed on a server that wasn't hardened then the normal webapp install is pretty much flawless and automatic.

I agree that DAW could do a better job for standard hardened setups such as Plesk, but that's another story.

A security hardened server makes it harder for the hackers to come in and play havoc, but it certainly also can make deployment a lot more tricky.
Especially when you don't know that such a setting was made and cannot access these settings by yourself.
--
Wil