I'm looking at the possible causal relationships between certain actions and resultant discomfort. As I understand your argument, you believe that certain actions by one person will always result in discomfort by the other. I disagree, and I submit that the discomfort is a product of the original action and its response. In other words, if someone has made you feel uncomfortable, it may be possible for you to reduce that discomfort independently of the precipitating action. Your discomfort may be due to an irrational bias. This would be a reason not to shun someone for making you feel uncomfortable.
There is a difference between analyzing an action and communicating that you are analyzing an action. To speak to your concluding example, "smiling back" and, "[going] in your head and think about whether or not that signal means that she likes you," are NOT mutually exclusive. With practice, you can do both at once. I would call this leveling up.
If you have a crush on someone you usually want to find out if they have one on you too. In my opinion outright asking them is often not a good solution, because if they don't have a crush on you yet it decreases the chance of this ever happening if they know you have one. This believe is based on what I read about love psychology. Hovever I don't really want to discuss the option of outright asking them in this thread, therefore I have not elaborated further how I got to this believe.
The alternative to asking them is trying to interpret signals that they might give you. However to know how many signals you need before you should believe that they are in love with you, you would need the prior. I have not been able to find anything about the prior of someone being in love with you. Therefore my Idea is to do a survey in order to find out how likely it is that a person you know has a crush on you. The plan is to ask the person taking the survey how many people they know well enough to possibly have a crush on them and how many people they actually have a crush on.
I have created a Survey for this and would be really happy if you would participate.
The next stepp would be to discuss how certain signals a person can give you raise the probability of them having a crush on you. That part is quite difficult. I think probably the best way would be to check how your friends react to certain situations and what body language they show you and then, if you find out someone has a crush on you, to look up what he did differently from people who are merely your friends. I am currently not in a good position to do this experiment but if someone wants to try or has results about this to share please do so. However I think this part is less important than finding the prior, because most people have at least a general idea about what certain signals mean from personal experience while at least I have no idea at all what the prior might be.