Hi,
I work for an international repro company which specialise in high end blue chip accounts.
We utilise Artpro and Illustrator for repro and adopt two workflows. We find that some files its more comercially viable to keep the file in illustrator and trap and process them through there.
For our illustrator workflow we utiise pre press plugins that are available. Have a look at
www.eskographics.com ,thier deskpack plugins for ai handles traping for both linework and CT to CT so its pretty good.
As always we have had good and bad results but if you need any further support in any of the applications please get in touch.
Thanks
E :P