Total Commander

Two bugs with copying.

1. Can't copy from ZIP archives to /system. Copying from a folder works fine. Copying from ZIP to /data or /sdcard works fine.
2. Can't replace existing files in /system. "Can't create target file". I need to delete the old file and only then copy.

Samsung Galaxy Nexus, 4.1.2, rooted.

1. Sorry, this is impossible. Apps cannot write directly to system. When you copy a normal file, TC actually calls a separate command line program started via the "su" (super user) command. This program then copies the file.
2. Currently this isn't supported, so you don't destroy important system files by accident.

1. Sorry, this is impossible. Apps cannot write directly to system.

But it would be possible to extract the file to a temporary folder in /data and then su it to system.

Yes, that would be possible. Currently you will have to do that yourself.