The basic translation of אבל is 'but'. However, it is also used, as Rashi says, as 'really'. It is the same word and the same literal meaning. The function of 'but' in this context is used to mean 'really'. In the language of Mishna we have the same thing: ברם זכור אותו איש לטוב, but this person should be remembered for good. But, as in, and how. In fact, in Yiddish we do the same. א מלמד, אָבֶּער א מלמד.
As for ואת, we must realize that Hebrew, especially biblical Hebrew, is not English. Every language has its own usage. In biblical Hebrew, the 'and' is often used in the beginning of a statement. Although the closest translation of the vav is and, it is not completely the same. The book of Shemos (Exodus) begins with a vav. It is a hook, saying, I mentioned first part, here is the second part.
In this case, after completing the statement about Yishmael, the next verse begins with And Yitzchok, which in this case, of beginning the statement, it read as and on the other hand, Yitzchok.
We must always remember not to take translations for granted. For example, we have the lamed prefix which is often translated as 'to'. However, as is evident in many places, it can also mean 'regarding'. It is not a different meaning. It is a pointer. Often it will mean 'he said to her', but it can also mean 'he said of her'.
Another example is 'send, you shall send'. This is the famous biblical syntax for emphasis. In English we would say 'you shall surely send'.