This particular word has gazillions of meanings and usages, so it's going to be confusing. But your examples are as follows.
So that you can be admitted quickly, please have your tickets ready.
This is correct but it's a bit of Yoda English. In normal case, I'd turn it around, just as you suggested. In fact, that's the proper way to use it, in my view. The way it's above, it puts a lot of focus on the reason why something should be done. A bit like this.
Please have your tickets ready, because - and here's the most important part that you should into consideration - that you can be admitted quickly.
Now, the next example is wrong. In the state it is now, by itself, it makes no sense.
So that is what you really think of me.
It can be made to work by precedence or succession of a context, like so.
I'm sensing suspicion, so that is what you really think of me.
So that is what you really think of me, I've heard from my friend.
But most likely, it's just a grammatical error and what you actually mean is this (note the comma and question mark). Still a bit cryptic without a context but it expresses the speaker's question of the listener's opinion, just as you guessed. Please note that the usage of really makes it sound as the opinion isn't favorable (but that's a slight hint only).
- So, that is what you really think of me?
- Based on the evident facts, that is what you really think of me?
- Inferring by the known circumstances, that is what you really think of me?
The usage of so here is equivalent to based on the evident facts... or inferring by the known circumstances. The difference is that the first one is colloquial and the others are formal.
So that is where I lost my book!
This can be interpreted in two ways, just as described above. The difference is rather slight (no wonder you're not seeing it). Here, you state a reason and draw a conclusion.
I know John's a thief, so that is where I lost my book!
But in this case, assuming it's known and agreed from elsewhere (or communicated somehow outside your statement) that John's a thief. It's still a conclusion but it's made based on more independent premise than just your words.
So, that is where I lost my book!
When you say: "it expresses the wonder of speaker that he lost his book in such a damn place", you're right. Because you refer to the known and agreed premise.
So, just to be clear, that is not the correct way to talk to your employer.
In the above example, I see that "so" refers to a previous conversation and the speaker means this:
As I explained previously what's an inappropriate conduct at the workplace, that is not the correct way to talk to your employer.
Note, however that this:
So, just to be clear, that is not the correct way to talk to your employer?
is totally different. It expresses surprise and request for verification from the previous speaker. A bit like so.
Are you rally saying, that is not the correct way to talk to your employer? (Because I find it too strict/weird/unsual etc.)