Do editors like having cumulative thesis papers published in the same journal? I am going to submit a manuscript that, if accepted, will be included in my Ph.D. cumulative thesis. The cumulative thesis will be composed of two papers: the first one has already been published in the same journal to which I am going to submit the second one. So, in the best case scenario, I will end up with a PhD thesis having two papers published in the same journal. The papers are somewhat linked but different.

Now, I am writing the cover letter to the editor and wondering if it is a good idea to mention this aspect. Could it be good, bad or irrelevant?
It is always important to acknowledge past publication history in any paper or thesis.  For example:


If any portion of your thesis has been published in any form (such as a technical report, conference paper, working paper, or journal paper), you must acknowledge that prior publication in your thesis.
If any portion of a journal submission has been published in any form (such as a technical report, conference paper, working paper, or PhD thesis), you must acknowledge that prior publication in your submission.


In both cases, the later publication must acknowledge the earlier one.  Some publication venues impose restrictions or conditions on the later publication of the same result.  For example, in many fields of computer science, conference papers can be republished in journals only after the addition of significant new material; in other fields, republishing conference papers in journals is simply impossible.  In chemistry, even submitting your PhD thesis to University Microfilms may publication of your thesis research in a journal impossible [source].  Conversely, some publishers require that any thesis that includes results from a published journal paper not only cite that paper but include a copyright notice for the repeated text [same source].

But there is no similar expectation that you acknowledge future publications, because they don't (yet) exist.  It's really none of the editor's business what you might put into your PhD thesis—that's entirely between you and your thesis committee.