Ah, I see everyone is talking on the other thread. My comments are pretty simple by comparison.
I would say that you will be best off accepting the separation of content rule. Its not just php but also for html and css, presentation and logic, and even js.
One person made an argument that the *system* should allow putting everything together, and that's fine, it doesn't mean any developer really will or should do that. Not if you want to get real code working well ;-)
The basic argument was that you can't debug your code well like this, but its also that you can't change anything easily, either. Changing any part of the code could affect other parts and could break stuff easily.
Php of the front end is a huge security risk, but its also better to separate css clearly from html, that way changes can be done easily, in one place. For js, there is no sense in loading a lot more than needed.
Its the same logic with snippets and chunks, they are letting you build a collection of tools that can go where you like, across templates, across domains, multiple times on every page, or whatever. Call them wherever you like, and adjust them in just one place.