They both work the same - there is a browser (IE based) and a webserver, but with ZZEE PHP GUI there is no TCP/IP interaction - an added security bonus - so they both true desktop application in your definition. If you mean that it looks like a browser, you just can switch the UI off.
As to encoding, ZZEE PHP GUI comes with bundled and preconfigured bcompiler - so your code can be compiled and hidden.
However ZZEE PHP GUI is more universal. If you, for example, wanted to write a simple script for yourself, like automating some files, then in case of PhpDock, you need to put it to the same dir where PhpDock is installed, and to run a PHP script you need to call phpdock's exe. What if you need to run two or three scripts? (You either need a second installation of phpdock or ...).
With ZZEE you don't have problems like that - you don't care where your PHP scripts are located or anything else. You just click a script - and it runs.
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