First, the zip file if modified in ANY way will fail the assertion check in recovery when you go to install it. So, while I rename the zips, you can rest assured they are direct from moto's servers unmodified. I rename them because too many people download "Blur_Version.5.9.905.XT875.Verizon.en.US.zip" and install it. What version is that? 229? 230? 232? 235? 238? 239? 242? From that filename, you have *NO FREAKING IDEA*. So my "suspicious" zip as you call it tells you what version it installs on top of, and what version you will end up on. This is by my design.
As for the inner workings of the House of Bionic, I've been over this all before. It's in my thread. It dynamically builds the menus so that it'll support any FXZ and set of updates without having to be rewritten. Believe me when I say that's challenging in a batch file. Once you select what you want (INSTALL or REINSTALL) then the appropriate RSD script is copied into the FXZ dir, certain files in the FXZ dir are backed up and replaced with files from the update you're installing as needed (i.e. the boot.img for an install, and MANY more files for a reinstall to build a mini-FXZ), and then I command line script calling RSD to flash the files to your phone. We intentionally throw an RSD error as the last command to force the phone to stay in AP Fastboot mode. The reason is we do *NOT* want the phone trying to reboot itself at this point as it will fail and require a battery pull. Next we have you boot into recovery and install the update. A cache wipe, and you're good to go. Then you can root it as needed.