Is the editor-in-chief's advice sincere? After submitting my paper to a reputable journal, the editor-in-chief sent me the following e-mail:

I am writing to let you know that I have briefly read your paper. It appears 
that your submission is better suited to (and will be better appreciated by) the
IEEE Transactions on X, or Y. I am, therefore, recommending that you submit it there.


Both recommendations are also reputable journals and since the work is inter-disciplinary, such a reply does not surprise me very much.

However, I wonder if I can interpret this also as a kind of quality evaluation for my work, because after all she recommended high-impact-factor journals?
Or am I reading to much into this and the only message is that this is off-topic for the particular journal.

In other words, is this a common type of response or do editors base their responses also on the quality of the work (e.g. recommending lower ranked journals, conferences or straight forward not to publish anywhere)?
I would not interpret the message as a statement about quality. If the editor felt your article was below par for the journal you will most likely get such a message. 

That journals reject papers because they are not suitable is not uncommon. In this case, as you say, the alternatives are also good quality publications and so it seems like good advice. The fact that the editor recommends these journals could actually mean that your paper is seen as suitable for publication in them and thus can be taken as a positive evaluation, however, not a guarantee for success.

I will finish by saying your editor does the job well. The alternative of accepting a paper for review although it may not be suitable for the journal could lead to a drawn out process leading to rejection and loss of much time.