The lack of customization is very bothersome however it does not need to end that way. The changes i'm about to suggest wouldn't be able to be added in a month and a half, but they should be more than possible to do after release, even as a reasonable priced DLC or ingame shop. (Most cosmetics should be unlocked via playing with only a few costing anything.)
I will start this by saying balance is far more important right now than customization. If the game has good balance with no cheese strats (tyranid assault craft spam, ork mega-roks, and necron star-pulse BS just to name a few) then customization is the secondary focus.
Remember how in the old game you could get favours for each ship? Since you can level up your faction fleet anyway there is a new system of favours that could work very well. Say you like playing as the Nurgle DeathGuard; as it stands your ships start out all warped and covered in tenactles.
A alternative way to do this would be that your ships start off looking like "normal" or slightly warped Chaos ships. As you play and level up with your fleet more and more ships in your fleet slowly change until they are fully covered in muck and tenactles. Same thing with Khorne where more skulls, brass, and daemonic icons are put on the ship.
I have a few ideas for other factions as well, like Imperial Navy ships having differnet colored engines, bigger auger arrays etc. Maybe you can put a bunch of Aeldari runes on your corsair fleet. You can have a bigga rammin gob on your ork vessel (it would be cosmetic and have no effect on gameplay)
Another major customization increase would be putting preset words and decals on your ships. If you have ever played Warthunder it would be a somewhat similar to that. In game a Retribution class has the two headed Aquila on top, maybe you can replace that with a statue of the Emperor, or a primarch, or whatever.
This is just the start. I mean there is all sorts of options we can go with each race and subfaction. What do you guys think?
Shoutout to valiran9 for making this post in another thread that seems to be what i'm trying to say.
An example of what I was talking about when I was referring to customizing Imperial ships can be found in some of the concept art done for the Anargo Sector Project, shown here:
Now obviously, for some modules like the midship variants, Luxury-pattern components, Surveyor-pattern prow, and Sprint-pattern engine, there would be definite mechanical differences. Nevertheless, I think the rest of the components easily illustrate how a ship could be differentiated from the rest of the group with a little bodywork.