My idea of a cool custom commuter is a frame that can take 30mm 700c wheels....can be fixed or geared....provisions for fenders and racks.....built for robustness over light weight.

Of course, having something like that is thiefbait.

So, you have to make a judgement about how thief-proof (not that such a thing exists) you want to make it. You could get a custom frame with no decals painted matte black or some other muted colour. You could get a nice custom frame painted exactly how you want it and hit it up with black electrical tape and sticker 'cammouflage'.

However, if you don't want to cry when the thing gets stolen, the only way to minimise that is ride any old cheap crap you can find.

Your solution is somewhere between those two extremes