Like last time, you're adding restrictions that aren't present in the code. Don't feel bad about it, Prolog is very different and it will take time to get used to it.
Let's start.
append([], L, L).
You said:
If the first list (L1) is empty and the second list (L2) is not empty then it is TRUE that the concatenation of L1*L2 is L2
In fact this rule says nothing about whether L2 is empty--or even a list!--or not. It simply says that the empty list appended to something else is that something else. Observe:
?- append([], foo, X).
X = foo.
The declarative reading here is "the empty list appended to L is L."
If the fact it is not true it means that the first list is not empty and so the concatenation of the first list and the second list it is not true that is the second list
Yes, this is correct, but Prolog isn't probing that deeply into the body. It just says "the first list is not empty, so this rule does not match; moving on."
The next rule:
myappend1([X|L1], L2, [X|L3]) :- myappend1(L1,L2,L3).
Your commentary seems excessively complex to me. I would say that this rule says: "myappend1 of the list [X followed by L1] to L2 is the list [X followed by L3], if myappend1 of the list L1 to L2 is L3." The consequences of this reading, however, are exactly as you describe.
Your understanding of what is happening in the first version is, therefore, correct.
The second solution is, mechanically, exactly the same as the first solution. The only difference is that we have moved the unification from the head of the clause into the body. This version is, to my eyes, clearly inferior, because all it has done is create extra work for the reader.
I think the problem you're having, so far, is that your declarative reasoning is intimately tied up with Prolog's engine of computation. A purer declarative reading like the ones I have supplied are simpler and look more like what the Prolog is saying (and have less to do with how it is evaluated).
It will take practice for you to separate these notions, but I think it will help you get better (clearly it's something you're concerned about). In the meantime there's nothing wrong with coming here and asking for help like you've been doing when you get confused. :)
Let me know if I can help more!