As the guy at Dynon that is tasked with thinking about these exact issues, let me offer my thoughts:
As we were all taught when we got our PPL:
1) Aviatie
2) Navigate
3) Communicate
The PFD part of your EFIS basically covers #1, and the MFD covers #2. So if your EFIS fails, the fact that you might lose your transponder or radio only affects #3. Your day only gets a little worse
At Dynon, we design all of our systems so if you have two screens, everything works normally on the failure of one. So if you were really IFR, you had a backup, right? If your backup was another SkyView screen, then you now use that screen to control the transponder. Nothing in the plane has changed except you have 1/2 the screen real estate and 1/2 the buttons. The workload goes up some, but not through the roof, and most of that workload is not due to the transponder, which you are not touching because you have your squawk already.
If you use a dissimilar backup like the Dynon EFIS-D6, then you do lose your transponder if you lose your only SkyView screen. However, this is not a flight critical loss. You might be limited to what airspaces you can enter, but that's about it.
Another issue is that almost everyone is already relying on their EFIS for the transponder even if they don't realize it. Probably 95% of experimental builders today use the EFIS as the altitude encoder for their transponder. This means that when the EFIS stops, so does the Mode-C altitude encoding. This is what you need to fly IFR or in controlled airspaces anyway, so unless you also put a standalone encoder in, you were already relying on the EFIS. On top of that, no matter how you control your transponder, you probably only have one of those. If it were a standalone transponder, it could have failed on it's own unless you are putting two transponders in.
So, the transponder is a case that when well engineered, you really may have increased reliability by having it integrated since you have more than one controller running it.
You can make all the same arguments for a integrated radio or audio control panel as well.
Where the radio and audio panel break down is in the User Interface. I actually think the UI for the transponder is great. You get 8 buttons and can just type in your Mode-A code really quick. No spinning knobs, and the 4 digits are pretty easy to remember when they are assigned in case you need to move across a menu or two to enter it.
I'm not as convinced with a radio or audio panel. I personally don't think that having to dig into a menu every time you want to enter a frequency, swap frequencies, or change the volume is a good user interface. When the controller says "change frequency to 128.975," I don't think you should need to hit BACK->BACK->RADIO->MHz->turn knob->KHz->Turn knob->Flip flop. If all you fly is VFR at uncontrolled airports, maybe the EFIS can always have a good suggestion ready for your next frequency and you can swap when you aren't busy, but if you are in any Class C or B airspaces, you're going to get given frequencies that nobody knew was coming.
I think the same is true of adjusting squelch, volume, and sources with an audio panel. When you want the volume changed, you want it NOW. You don't want to have to go into a menu.
Because of this, the radio that Dynon is working on will have a control panel, and will require it to operate. The reason for this is not because of redundancy, it's because the UI is right. It will use SkyView to give the control panel all sorts of amazing features, but the control panel will also give you exactly the knob or button you want all the time.
It does also give you redundancy as well, which does have moments where it's nice. If you do lose all your EFIS units, at least you can still communicate, and I think the radio is something more likely to save someone when their EFIS fails in IMC than their transponder is.
I think the real question builders should ask is what happens to their workload if a device in the plane fails. Accident and human factors studies will tell you over and over that workload is a big deal for safety in a plane. So, the real issue with the "eggs in one basket" design is if the loss of the basket causes your workload to be come unacceptably high.
So ask yourself: If I lose my EFIS in my kind of flying (VFR, IFR, IMC), how big of a deal is that? For some people, the loss of attitude, altitude and airspeed may hardly bother them since it's bright and sunny out. In this case, the loss of the transponder along with it is probably a non-issue. The radio might actually be the most annoying thing to lose in this case, and losing your intercom so you can't talk to the non-pilot next to you and explain the situation will be annoying as well. But neither of those is a saftey of flight issue until the co-pilot starts punching you in the shoulder trying to get your attention.
If you're in IMC, then losing your EFIS is a big deal. No PFD, no EMS. That will make any IMC pilot nervous. But, you likely still have your navigation (Certified GPS), and you have some sort of backup airspeed, altitude, and attitude. Here, the loss of the transponder is annoying, but unlikely to lead to any real workload increase. Again though, the radio is a larger loss and is doubled if you lost your transponder and can't squawk the no radio code. If you were tied to an integrated audio panel, this could actually be a big issue, because all you will have access to is your primary COM radio, so you may lose other sources you were used to having.
I'm sure some EFIS vendors can integrate a radio better or worse than others depending on what kind of knobs, and buttons their hardware has. There is no single answer, you have to evaluate how you fly, where you fly, and exactly what your system configuration gives you in various failures. For Dynon, for our average customer, we believe the transponder can be remote, but a radio or audio panel needs to be it's own module. That's right for a large group of customers, but will inevitably be wrong for some. There are good arguments each way, and thankfully the market is giving builders options to chose what is right for them.
--Ian Jordan
Chief Systems Architect
Dynon Avionics