Using HTTPService directly is a fine way to go if that's what you are comfortable with. There are several benefits of doing the data services and the code gen route, but it's up to you whether they are compelling for your use case. The first benefit is strong typing on the ActionScript side and being able to easily do data binding to your UI elements. This should likely make development go more quickly for you. Another benefit is the built in support for paging and client-side data management. Those can be really helpful for large data sets and improving performance, as well as for batching up edits on the client-side instead of having to submit edits one at a time.
If you do use the DCD features, you should not be at all restricted to the kind of PHP classes you write, so you should still be able to secure it the way you want to. Were you finding a restriction there? We'd be interested to hear what issues you encountered if you did write a custom class and we weren't able to introspect it, or you weren't able to secure it the way you wanted to...
As for Flash Builder for PHP, some people might say the integrated debugging alone is worth the upgrade. It makes debugging the ActionScript and PHP much quicker and it's easier to track down issues. It's also helpful to have the project wizards set up the linked Flex and PHP projects for you so that it's not so manual setting up the Flex project to point to the PHP server, etc. Also, if you do go with DCD features over plain HTTPService, the introspection for the PHP classes is done via Zend Studio's code intelligence, so you have way fewer steps to building the strongly typed ActionScript value objects and services. So overall, I'd say FBPHP is about improving productivity when working with Flex and PHP together. Hope this info was helpful for your decision!