It is not ideal practice unless clear justification is given. The authors deserve transparency and detailed reasoning, particularly after undergoing major revisions or desk rejections. Many of us recieve rejection email stating lack of novelty but in scope of the journal or out of scope in just two to three lines only. That’s really unfair.

1. Desk Rejection After Major Revision

It is not uncommon for editors to check for themselves if requests for major revisions were followed by the authors. This can speed up the review process. However, the only legitimate reason for editors to reject your paper at this stage would be that you were unable to comply with the demands of the reviewers, i.e. that you did not manage to revise your paper in line with the reivews. Reference to aims and scope of the journal at this stage is problematic because this should have been checked prior to assinging reviewers.

2. Rejection with Invitation to Resubmit, Then Desk Rejection

This cannot be assessed because we know only that in your opinion, your revised paper meets the aims and scope of the journal. There are at least two possible reasons for the rejection:

1) You correctly followed the recommendations of the first editor but the two editors have different opinions on the aims and scope of the journal (which is not unlikely, they are different researchers with different scientific perspectives, after all).

2) You believe to have followed the recommendations of the first editor correctly but your scientific perspective deviates from those of the editors and your paper still doesn't match the aims and scope of the journal.

In both cases, you can write to the editors and ask for clarification. I would recommend this in the second case. Write to both editors and quote the email from the first editor. Let them discuss this between themselves.

I can mention both journal names, though my intention is not to criticize them but to highlight a pattern I have observed and wish to understand the possibilities... In both cases, I sent emails to the editorial team, but due to the publisher’s new policy, all correspondence is now routed through a help desk, which handles further actions. In one case, I received a response stating that the manuscript does not align with the journal’s scope..a conclusion that seems completely different from the initial decision and regarding the concerns raised by the reviewers, I can say based on my experience, I believe we did our best to address all reviewer comments and were genuinely expecting an acceptance. In the second case, I have yet to receive any response, and I do not anticipate one will arrive.

Well, this sounds unsatisfying and this kind of response is cleary a failure of the journal. Apparently, you had a question about procedure and they answered with a canned response about content. You could of course refer them to the committee on publication ethics:

https://publicationethics.org/

Sir, Thank you for your reply. I did exactly the same, I received that response only after the matter was referred to the ethical team. However, my team felt it was a waste of time, as even after 25–30 days, the outcome was the same. So, I sent a final email thanking them and stating that I did not wish to pursue further discussion, as it was unlikely to lead to any outcome. As a conclusion, personally, I completely removed that journal from my list for future submissions (case 1).