As you say, it very much comes down to whatever the producers and writers find convenient at the time.
This is TV fiction, nothing more, nothing less. They don’t seem too concerned about the absolute logical consequences of everything that happens.
Overall, this production team only really seems interested in what works for them in terms of telling that story *in the moment.* Folks stopping afterwards to think, “hey, hang on a minute, what about [x]...?” really doesn’t seem to matter that much to them. They either understand the inconsistencies and just don’t care or they’re not even bothering to make the effort to think things through.
My overall impression is that there seems to be a lot of “Hey, wouldn’t it be cool if...” and not much thought beyond that. Adding the “-A” suffix may well be one of those things. Given the historical significance of Starfleet registry suffixes in the Trek universe, it’s odd that they did it and there was NO mention at all in the dialogue.
On they other hand, maybe it’s simething else entirely: perhaps this is something the CGI FX team threw in during post-production and do the writing team were unaware of it? Indeed, it may not have even been considered at the time they were shooting the third season.
Anyway, all this stuff is mostly fairly minor and you can just shrug, maintain suspension of disbelief, stay in the moment and move on with the story of that episode; occasionally they do something very jarring that completely drags you out of the moment and is very disruptive to staying with the story-telling.
We all have different thresholds for that sort of thing. I truly disliked the whole Tilly-as-XO thing and found it entirely unbelievable and very jarring but I’m totally happy to accept that others were just not that bothered by it or even liked the idea.
I don’t imagine this approach is going to change as the series moves forward...