Assuming that all you say is correct, if Apple are embarrassed by spec sheet comparisons, why not just bung more RAM in anyway and have done with it? RAM is cheap and you can never have 'too much' of it, so it would be win/win. If necessary charge an extra $20 for the phone, nobody would baulk at that.
No idea, I'm not Apple. I don't give excuses in the matter - like I said, it's very little money and additional power draw. Maybe they want to hold it for differentiation for the 6S/Plus. Maybe something with the fabrication required very specific chips. Maybe they just had a lot of 1GB chips left over. It's really hard to say. All poor excuses to boot.
I just think that RAM shouldn't be the final purchase determining factor unless you are in a very specific, high-RAM utilization workflow, such as the several tabs & switching scenario I outlined. The A7 (and A8) are just dual-core CPUs at a bit over 1GHZ, but smoke the competition in most tasks. It's all about the combination of hardware with software perfectly tailored for it and close to the metal.
You can't uniformly compare numbers is my argument, I suppose. It's not like new apps will run slower or something, developers can only develop against the resources they'll have. Right now, 1GB is (likely, need teardown) the max you can get on an iPhone, so that's the most they can account for when developing apps.