Automator's "Combine PDF Pages" action doesn't preserve crop?
There is a package called pdfjoin which uses pdflatex to combine pdf files. You could try joining your pdf's in the following way:

pdfjoin 01.pdf 02.pdf


which will combine the files into a single pdf called 02-combined.pdf, in your current working directory.

If you don't have LaTeX installed you can follow this guide to do so. 

This preserved crops for me when I tried. If you can get this working on your system, you could then maybe look at putting this together in a bash script.