Well, for starters, no, not all customisation is micro transaction. Every class has separate reward path for leveling it up, and every one of those classes give you some items to customize your character and ship, whether it's costume pieces or dyes. Unfortunately there's no official list of the available rewards depending on the level, and noone decided to put any effort in making one as well, so I can't really tell you what will you get. All I can say is that you can get the costumes through leveling, so just keep playing!
Also, every Tuesday and Thursday at 8pm CEST there's an hour of DevMatches, where you have a chance of getting into if you type down the password that's gonna show up on globacl chat fast enough to join the lobby. If you win during those games, you can take a screenshot of your victory, send it to proper developer via e-mail (currently greyt@musegames.com) and ask for one of the items from the store that you could otherwise purchase.
Other than that there are also costume pieces that Devs give to everyone once in a while. If you buy a GoIO 4-pack you(and your friends) are rewarded with a single costume piece for every class. There are also event-related items that everyone gets, like a halloween mask or christmas hat, as well as stuff given to everyone as a celebration of f.e. Pewdiepie's video about Guns of Icarus Online.
Keep in mind, though, that MuseGames is not as big a company as Riot Games, Square Enix or even Hi-Rez Studios (YET), and they need the support to keep the buisness going. Even I, being a person from rather poor country with really bad currency ratio, spent a little bit more on costumes to help the guys (despide the fact I could get it from DevMatch rewards, being on almost every DevMatch since January), they do deserve it :>