This is just how shape layers work - they are a comp sized container inside which the vector paths are rasterized. Feeel free to structure your work by using groups inside the shape layer hierarchy.
I don't believe that is correct. I've worked with vectors that were converted to shape layers before. Their containers were not comp sized upon conversion. In fact, I've done it with the same files in the past.
Here is a screenshot of multiple shape layers that are selected. Their containers and handles are limited to the size of the shape layers, not the comp.
let's try to isolate the problem. there are many reasons why your Ai objects will not be important correctly. first make sure you are using the recommended workflow to importing your Ai files to Ae: Preparing and importing still images in After Effects
not related to your case, take into consideration this helpful advice by our very own tribe elder Rick Gerard:
Unless you specifically need to use shape animators on your illustrator files there is absolutely no reason to covert the vectors to shapes.
if you are still having problems, reduce your Ai file to just the layers that are causing you issues and are imported as Composition size no matter what, and we could look into this further. you can also upload your Ai file.
Hi Roei, thanks for the reply.
I finally found what the problem was!
The problem will appear your object in AI files have opacity below 100%.
You can see here clearly: https://dl.dropboxusercontent.com/u/63499976/shape_convert_folder.zip
Solution: don't make any object in AI transparent before you import to AE.
(repost from other thread)