Is it good to have all the PhD publications in one journal
For the PhD itself it probably doesn't matter a lot, but if you are looking for a further research career, I'd advise diversifying a bit. It has the following advantages:


Other people may have another "favorite" journal, and if you have published in multiple journals, you increase the chances of people thinking "wow, she published in xyz!".
You will get a broader readership and generally more visibility if you publish in different journals.
There is some risk that people may see your research as too narrow if you only publish it in one single journal.


Maybe you can try adjusting the framing of your research problem a bit, so that another journal will become a better fit for it, and then try to convince your supervisor by comparing the scopes of journals and arguing why this paper fits better to the other journal.