Like I keep saying, I totally understand that I am almost completely inexperienced, so these scenarios may just be completely unrealistic. If they are, just tell me.
You are asking very reasonable questions. Good for you. Keep it up. The way most of us learn is by asking questions, and then coupling that with a bit of trial and error. I would much rather have students ask me a question in an OW course, than to have them complain later that they 'didn't learn that' - because they didn't ask.
To answer your original questions: 1) I do not find having a second stage on a bungee necklace to be in any way annoying, or cumbersome or uncomfortable. I also did find, at first, that having my mask down around my neck was annoying and felt uncomfortable, and that took getting used to. Now, I routinely lower my mask around my neck at the surface - often to read my slates - and think nothing of it. It is really a matter of practice and accommodation; 2) I have never tried running a short alternate hose over my shoulder ('
Does anyone ever put their alternate 2nd stage on the same 22 or 24" inch hose (like for a necklace), but then run it over the right shoulder and down to some kind of octo keeper') and down to an alternate holder on my chest. My alternate hose goes over my right shoulder when I use a bungee necklace (usually a 22" hose). It goes under my right armpit when using the more 'traditional' configuration (40" hose), and the second stage hose is either clipped somewhere or inserted in a pocket designed for that purpose on my BCD (Aqualung Wave). If I am going to donate a second stage other than what is in my mouth, a 22" hose would be quite awkward - for me.
In your case, I would suggest you try both - put a second stage on a bungee necklace, and see what it feels like, and try running the alternate hose OVER you right shoulder and clipping it somewhere, instead of under your shoulder. Notwithstanding the fact that there is a bit of chest-thumping here in SB at times, and that many of use have our definite preferences, you are free to try different approaches, to see what suits you. You would be better served to try a bungeed necklace configuration, even if you ultimately decide it is annoying / cumbersome / etc. - for you - than to presume it is (or isn't) without trying it.
So, it seems like if one wants to be best prepared for any kind of OOA situation (remember: in REC diving), one would recognize that you really can't predict what the OOA diver will do and so you'd want to be prepared for them to use either of your 2nd stages (in case they just swim up and grab one).
That is a very good point - there is an element of unpredictability. True OOA situations are quite rare. And, what you usually read, regarding behavior of OOA divers, is supposition or is based on single anecdotal experiences. That is actually good, that OOA situations are so uncommon that we don't have a database that reliably predicts diver behavior. The diver who is 'aware' enough to be calm, cool, and collected when coming up to you because s/he is OOA, is also the diver who would be 'aware' enough to not get into such a situation anyway. Certainly, predictability can be increased by a good pre-dive buddy check, where the divers review each other's equipment configuration, and agree a procedure (active donation vs passive retrieval, donation of primary vs alternate second stage, etc.). I don't want to have to rely on their memory of their training, I would rather have them rely on (their memory of) what we agreed just a few minutes earlier. OK, to be perfectly frank, I would prefer to always dive with people whose training was so good, and who routinely practice skills they learned in that primary training, that their reactions and behaviors are instinctive, predictable, and involve muscle memory. But, I would also prefer to have peace on earth, freedom from disease, goodwill to all, etc. Therefore, I am used to disappointment and I prefer to rely on what we went over in the briefing.
On some reg sets, I have a yellow 40" hose, and a second stage with a yellow purge cover. Since that (yellow purge cover second stage) is what I am breathing from when they go OOA (simulate it), it becomes pretty apparent which one they should go for. Most of my regs do not have yellow hoses or covers - they are black. But, for an OOA diver to grab the bungee necklace reg that is under my chin, and at least partially obscured / blocked by the second stage that is in my mouth, would take a bit of effort, more than I would expect from a stressed OOA diver.
Of those, just 1 or 2 or 3 were using the reg necklace setup. And no, that is not how they were teaching it. All the students had the typical octo clipped to BC and we were taught to pass the octo to the OOA diver - not pass the primary and use the alternate for ourselves.
There are a number of university-based OW training programs in which common (I hesitate to use 'standard') hose lengths are used - often a 30" and a 40" second stage hose - and one second stage, on the shorter hose, is put on a bungee necklace, and the diver breathes from the second stage on the 40" hose as their primary. For OOA situations (drills in the OW course), the diver donates the second stage in their mouth, then go to the second stage on the bungee necklace as their back-up. It works, and well. I was introduced to that approach when I conducted OW dives for a referral student. I now use configuration that for private OW students.