The cargo net is because of the battery I think... the anchor points just aren't there because some of them on the non-hybrid are on the floor. On the hybrid... they'd be attached to the top of the battery which is the floor.
The running boards is curious to me. I've been under the car and the coolant and power lines for the battery do run NEAR where the running boards would anchor... but I could have sworn they were an option then they weren't for the 06...
The mirror? I haven't the foggiest.. in fact I think a couple of people have ignored it and installed them anyway.
There are notes in the FEH workshop manual that talk about problems with certain readouts, trouble codes etc. and possible reasons. Adding equipment is a big factor with some of the issues and problems with the FEH. There are reasons such as things with the key chip in the 05, auto locks etc, that could not be resolved, so they were deleted.
The Powertrain Control module and other computer controls modules in the FEH may be effected by add on equipment. For this reason, I would only add equipment that is approved in the use of the FEH. The only things in my FEH that I've added is the Scangauge and full spare. You may not know it, but you may have problems with the warranty by just adding that mirror or non stock equipment.
Weight and drag seem to be factors for some of the exclusions. I added OEM step bars within a week after I got my 2006 FEH. They bolted onto fittings in the frame just like the instructions said they would. The weight penalty is worth it to me as they make getting in and out of the car much easier for my 5-year-old daughter and her grandparents. I also added a receiver-type trailer hitch so I can carry my bicycles on a rack behind the vehicle. The manual states that the vehicle is capable of towing 1000 pounds, so it could be used to tow a small trailer (at a considerable hit in efficiency, I'm sure). The hitches that are specifically made for the hybrid are designed to not interfere with the battery AC lines.
You may be right about some of the electronic add-ons, but I really miss the outside temperature display that I had in my '98 Explorer.
I can't think of a single reason why adding a Gentek mirror would void the warranty(& I've worked in the car business for years).
All the mirror needs to work is a 12v power source, it's no different than plugging something into the factory supplied 12v power outlets.
The only thing I can think of is that any electronics that take power from either battery would also force you to take some kind of hit to FE. After all the 12V battery can only get charged when the ICE is running. Whereas the 330V battery gets charged by either re-generative braking or by running the ICE. Remember all vehicle power/accessories gets their power from the 12V battery.
As mentioned, the MMH has the auto-dim mirror, but without the Homelink (garage) feature.
The CD-based NAV system is too old of a design to support Bluetooth (Ford's MobileEase), Satellite (SIRIUS), or Ipod (Ford's TripTunes) features, even as a dealer installed option. There is really no reason why the LCD display could not, selectively, display these other sources of info. As a side, I really wish that the Premium Pkg allowed one to "downgrade" to the Audiophile system which DOES support all these things.