I, too, find I'm better at that kind of thing in hindsight. At the time, I'm not very good at interpreting and 'reading between the lines', because like you I tend to take things very literally, but afterwards when I think about things and analyse them I think it's possible to do as you did, realise the underlying meaning.
I think that's good, because it means you have insight and are capable of empathy (it's just running in a slightly later Aspie time zone to the NT time zone!). It's good that you're capable of putting yourself in someone's else shoes and wondering about what they might have been feeling and what they might have meant.
I think many Aspies don't have that kind of innate awareness that NTs have of what people actually mean, but some Aspies are capable of learning by example and trial and error. It's like NTs come pre-programmed with a complete systems analysis flow chart whereby they encounter a situation and they know what the possible outcomes/options are and they recognise them and respond accordingly.
Girl comments on how it's boring to lunch alone:
> she's simply making small talk because it's kind of expected in the NT world to engage in inane chitchat in those kinds of situations
> she's having a low-level moan about working conditions to a colleague and looking for a sympathetic response
> she's looking for a lunch companion and > she's not inviting you to lunch or > she's inviting you to lunch
Whereas Aspies come with a less sophisticated version:
Girl comments on how it's boring to lunch alone:
> Someone's made a verbal proposition: It's boring to lunch alone. What do I think? Is it boring to lunch alone? Or is it not boring to lunch alone? Hmmm, I think so too, it is boring to lunch alone. I'll say "yeah..."
But the good thing is that now you're aware of the existence of the NT version of the 'flow chart relating to a person saying "It's boring to lunch alone"' you're aware of the other possible outcomes, so next time you encounter that situation, you can respond accordingly.
But the likelihood of someone making that exact same comment in that exact same scenario are slim, so how useful can this be to every day life? The advanced level of Aspie/NT communications is being able to apply those lessons to other similar scenarios, which means interpreting situations and assessing how similar or dissimilar they are to situations previously encountered, and thinking about whether lessons previously learned during or in the aftermath of earlier situations can be applied.
I think NTs communicate by just 'knowing' all those things, whereas Aspies can be a bit slow and they have to actually think through the processes, they can stall or hit a glitch, if they don't know about other options like underlying meanings.
I guess another analogy Aspies might relate to is video gaming. It's like NTs already know about all the secret doors and eggs. Aspies are fumbling through the game and only realise where they are when they stumble across them. But they can store that knowledge away for next time and use it then, they can accumulate the kind of knowledge NTs already have, through trial and error.