Hello,
1. Standard Missed Approach is exactly that...standard, and therefore based on two engines.
2. Yes, they take into account obstacle clearance, hence the reason APG data is far more limiting than the AFM. I'm surprised you didn't just send a quick email to APG to ask this? Therefore you have a definitive answer to refer back to.
so to answer 4, ask APG! The acceleration altitude varies according to A/C type, so may not always be relevant, depending on the weight/performance combination.
Best of luck ;-)