1) For this I would recommend you generate an FCP XML, which can be imported into Premiere Pro. The SDK doesn't provide control over project items.
2) You can see supported transitions and effects here: http://help.adobe.com/en_US/premierepro/cs/using/WSd9957a95a81082eb28f05af5126718c47be-800 0.html#WSd9957a95a81082eb28f05af5126718c47be-7ffd
3) Markers in the FCP XML can't currently be imported directly as Encore Chapter markers, but once the markers are brought in, it is fairly simply to switch them from regular markers to Encore Chapter markers. Bringing them in directly as Encore Chapter markers could be a good feature request, if you decide to use the FCP XML route - http://www.adobe.com/go/wish
4) Triggering an Export to Encore is not something a plug-in or external application can do. But by generating the FCP XML in advance, that should save a ton of time with the editing up front.
Thank you so much for your fast answer and very helpful links. The FCP-XML route sounds like the right choice. I am a little sad to hear that there is no documentation about the prproj-fileformat. It seems to be kind of a XML-structure and would in theory be automatical producable (at least in my mind ^^) as well !? Great help with the precise explanation about the markers and it would probably be worth a feature request. One last question about the export to a DVD, Encore seems to be the best choice but not controllable via script or plugin. Is there any DVD-authoring software capable of automating parts of the creation process? I mean like reading the prproj file and check how many chapters and choose a special theme...?