Ill say yes to the first one, although it will be limited. I was thinking everyone would receive an extra cypher, and of course their Defensers would be equipped with giant versions of your PC's weapons (that can't be cheap).
The second question...When damaged Defensers return from a sortie, a cloth is thrown over them as the runner disembarks. They are also maintenanced in a location that you do not know. These measures are to protect runners from 'latent radiation', according to the higher ups. I'll have to say no to customization for the Type-12s for now. It's something I plan to definitely incorporate, but there are strong story reasons why not. Sorry, that's all I can say.
I will also say that your Zorahi is armored with almost EVERYTHING, so if it would make you happy, you could describe your unit having something like a striped hide to cover the shoulder armor. Senpaiki's 'Soniku' has it's name on a roof of a house, and is painted pink.
You could also find bits out in the fields or beyond to help your unit, and the enigmatic fixers back home will grudgingly agree to try to graft it on, albeit in a place where you can't watch. Trying to modify the Defenser other than aesthetically in Gurrain without the fixers, however, is "dangerous to your health and illegal". You can't requisition Defenser mods for now, the fixers say they are "in short supply" and also don't want to do the extra work.
Hope this helps! Thanks for the questions, they have been very useful in building the world.