Why do we suddenly need a whole new system to do the exact same thing in parallel with the current system?
It's a good question.
One reason might be that (especially) system names are much more visible, appearing on the galaxy map, available through searching there, and (I think anyway) should be permanent in principle, or at least not changeable on a whim. Also, system/colony names carry a bit more weight than ship / FC names "diegetically" or in terms of the feel of being in a future version of the galaxy. FCs and ships move around, systems and settlements don't. Settlements and system names come up in missions, faction names, maybe weekly PP assignments...
In general: the name of a system or settlement is going to have way more impact on you as a player than a FC or ship name.
Don't get me wrong, I'm personally all for bizarre names - I see no reason why the Galaxy shouldn't contain people who name a planet "Stapled Peacock Flesh", it's a big galaxy after all, and if anything I'd like more of this weirdness, but the way I'd think about a system name or a settlement name is different to the way I'd think about a ship name.
I don't like seeing FCs named "FDEV sux0rs" and similar, but wouldn't consider reporting it. A system or settlement with that sort of name, though, should ideally just never exist in the first place IMO. The range of acceptable names in colonisation is therefore narrower for me than the range for ship names, and I expect I'm not alone in this.
If this seems odd, maybe consider if you feel there's a different range for system chat than there is for ship/FC names. My impression is there's a lot more leeway for expression (let's call it) in system chat, which I'd guess is because of its highly localised and ephemeral nature. Personally I've winced and ignored stuff in sys chat that I might complain about as a ship name (I've never complained about either so far.)
But having said all that, for namers there should IMO be a reasonable expectation that once your name is in place it will stay there; only fair to the coloniser who's put in the effort and taken on the burden of adding something permanent to our shared galaxy, and to others who might use the name as a reference point. Not to mention names changing in the middle of missions, BGS wars, PP assignments...
The situation struck me as similar to domain naming in the early days of the commercial internet and led me to outline a colony naming version of that system, which worked well in practice for little more effort than reading a few upcoming names on a mailing list every now and then (I'm not suggesting a mailing list!) Apart from technical overheads, the main problem is likely to be over-enthused guardians of naming purity objecting too much, which is why public guidelines are so crfitical (this was also true for the domain name thing iirc).
Like I said I wouldn't expect such a system to be actually put in place, but it's an interesting thought experiment to tease out some of the issues lurking behind an apparently simple problem, IMO.