Huh, I've apparently totally missed that. But I have three "rebuttals," if you will..
1) Then why do the TW-6 guys always fly around w/ their JANAPs? That's a rhetorical question, but an example of how it's not followed. I know it's AF, but I always hear the jet guys using their callsigns en route, as well.
2) This does NOT preclude the use of JANAPs when in the local area, which is already done all the time when VFR. So why must a callsign be changed by ATC from POOPSHOOT 101 to VV PS 101 when I'm flying in the same airspace, which is where my main pet peeve comes in. Again, I perceive it to be a carry over from the TRACOM. The TW-5 FWOP states flights outside the local area will utilize their ECHO number, but doesn't say anything about being REQUIRED to use it when flying IFR w/ in A-292. However, a common misconception was that it was required.
3) As I alluded to, sometimes tail codes aren't conducive to the ATC environment. A perfect example is NW. ATC sees a NW 600 on their screen. There's no NorthWest 600 on their strip, so they delete it out of the system. Then when you check in or call, they have no idea who you are. Yes, this actually happens and has been a problem in my current squadron.
I've had another situation where I was flying aircraft that had no tailcode. Well, a more accurate statement was probably that no one in that command knew what their code was since they hadn't ever owned aircraft before and didn't know how to look it up in the pub. As a result, flying w/ a code just wasn't done. I will say that you get better handling when you have "NAVY" in front of your callsign than if you're just some random callsign in a non-tactical aircraft.
All that said, HH, thanks for the citation. Like I mentioned, I totally missed that paragraph. I have no evidence to back this up, but I have a feeling the genesis of that paragraph is due to the way the ancient ATC system handles alphanumerics. If you're aware of the limit and write your callsign down appropriately (ASSHAT -> ASSHT) then the problem is mostly solved. That's what I end up doing w/ my current callsign and it works fine.