VW gas WAY too many motor options for these Beetles and I have never tried to figure out why and what the differences are.
This being said, checking my Bentley it shows 3 different 2.0L engine codes for the 2003 Beetle.
The non vert shows both the AVH & AZG engine as available.
The vert shows only the BDC engine.
I would search Wiki and see what useful info you may be able to find. Again how accurate will the Wiki info be??
My guess is there may be something different with the cylinder head/camshaft for torque due to the vert being slightly heavier and/or maybe something that allows the vert to be a 50 state emission compliant car??
This thread may be helpful?
http://newbeetle.org/forums/2-0-liter-gas/32449-2-0l-avh-bcd.html
I guess if you get with the parts department and check cylinder head casting numbers, camshafts and other things.
You may want to try and also get pictures of both your engine from the top and compare to non verts to see if there are different emission, vacuum and fuel routing.
Good luck, I have a 2003 1.8t vert and I know my engine is not really different but the engine code does sometimes cause issues with parts.