The differences in plugin APIs are in two areas:
- if Reader doesn't have the functionality, then the API isn't there. (eg. AVConversion)
- if the API modifies the PDF in some way, such as PDEdit
The browser plugin is a shim on top of whatever PDF viewer (Acrobat or Reader) you have installed. And it DOES run whatever plugins are installed. (however, you a plugin can choose if it wants to allow that or not)