So, in short, an option to tune to Clearance does show up under Ground Services, but selecting it simply boots you up a level in the menu hierarchy without contacting Clearance?
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Yes, it does what it does at a towered airport, minus the actual option to request the IFR clearance. Clearance are on call divert. 
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This is what I get on the ATC menu when I load C&D at KPRB (uncontrolled) and program a simple flight plan to KSBA.
If I tune UNICOM on 123.0 I get this:
So that place has no Ground. So it would need to have at least Ground to allow the Clearance option at all, or Asobo need to get Clearance out from under Ground, and make it its own thing separate from others?
Correct, an uncontrolled airport has no Tower and, therefore, no Ground.
In the case of KPRB, you would tune Hawthorne at 122.400 and request IFR clearance.
Here’s the same thing having pre-programed the same flight plan via the World Map:
Note that tuning to “Traffic on 123.000” has been replaced with “Tune Hawthorne Radio on 122.400”.
Once you’ve gotten Clearance, it’s good for .5 hour and the prompt to tune Traffic is, once again, available.
Again, however, you must use the World Map to receive this prompt.
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Clearance from Ground, or at a non towered airport, clearance by Phone
( no need to tune radio, and lets avoid the complications of getting the correct phone number 
)
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In real life at most untowered airports I had to either file via FSS and receive a clearance void time, or do the same directly via cell phone. Often I think that was more a problem with signal strength than anything else.
After entering the flight plan via WT at KPRB can you take off and pick up a clearance in the air, or is that option also not there??
Provided that was possible wx wise, that was usually the option I used IRL. File the plan via FSS or later ForeFlight etc, and then simply take off VFR and get the clearances in the air.
No. The problem remains even once aloft. I can request flight following, but there will be no option for IFR clearance.
I share your opinion, you are not the only one in this matter, many other have given up. The complexity of programming so many different options are difficult if you do not have the help of a real professional in the matter, like a retired ATC controller as you put it. X- Plane is in the same position. Better using Vatsim or similar 3rd party service if you want to have an approximate feeling (being generous) to the real world.
I have to wonder what an ATC Options Flow Diagram (State Diagram) would look like, if in fact, it has ever been expressed that way for visibility.
If such a thing exists, documentation of it in the SDK, would make a lot of the ATC’s Logic a lot clearer to all, and allow a far more informed discussion about it, and its pros & cons.
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I just tested it myself out of GCGM and there also was no option to request the IFR clearance once in the air. At least that should be possible in a modern simulator.
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- X plane is worse, actually much worse, when it comes to the built in ATC.
- VATSIM can be much better, of course, but it also has a major limiting factor…I have to fly where someone is willing to provide ATC services. So that is at least for me not an option.
- FS9/FSX was actually much better in many aspects of ATC than MSFS. And that is for me the most frustrating thing…simply go back to what already worked in the series. Then improve where possible.
Because almost all the complaints about ATC are 99% the same as from day 1.
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