Paulilf
The request not to transfer a potentially live ejection seat onto another vessel could just have been the fact that they did not know how to handle it safely and were reluctant to take the risk. A small fishing vessel probably would have stored the seat on deck until arriving in port, a naval vessel without much open desk space would have had to store it below decks which means a bigger risk to personnel if it even partially fires off.
The cold truth may be that the skipper of the naval vessal was not prepared to risk his own crew. However these thoughts would not have been articulated at the time and the intent may have been lost in translation, perhaps over poor channels of communication.
Is there not maritime law preventing or limiting the transfer of live munitions between vessels under way? That may give some insight into the reasons why the order was given rather than some deeper conspiracy.
All I can add is that I was always very careful around ejection seats when they were supposed to be in the safe state (i.e. safety devices have been fitted to prevent operation), I wouldn't go anywhere near one when it was in the armed state (i.e. no safety devices).
All this analysis would not have been reported in a newspaper, and in general (with no disrespect to the reporters) those who write the story do not necessarily have the technical background to understand what they write. Bracken / Brecon sounds the same, but the fact that the incorrect name was used may just be that no-one bothered to check the facts before the story was printed