If you get the md5 sum right editing the tar should work.
You can edit the downloaded zip before you flash it and it will still install. But editing after install is about the same amount of work.
What I used to do on the Nook Color was to modify the gapps zip to add the /system changes I wanted and then reflashed the gapps every time I flashed a new ROM. That way gapps were refreshed and the new changes were inserted in /system. Or, you could make your own zip to flash only your changes. The easiest way to make one is to edit the gapps zip to put your changes in and then delete the gapps files from the zip.
Do these zip changes with archive software without totally unzipping and rezipping.
Edit: Since some of my changes were modifications to build.prop, I developed a script to edit the new ROM's build.prop on the fly as part of the zip. That way build date, etc stayed right. If you want, I can use PM to send you a copy of my old edited gapps for you to study. However, since you are on CM10.1 stable, you will probably not be updating again.
Sent from my Nook HD+ running CM10.1 on emmc.
See my Nook Color Tips Thread here
and my Nook Color EMMC Partition Repair Thread here
and my Nook Color Updated CM SD Installation Instructions here
and my Nook HD/HD+ stock tips thread here
and my Nook HD/HD+ CWM Root Tools thread here