On two of my hardtailed bikes, I made a battery holder which can best be described as a basket or bracket rather than a box. Here is a picture from the XS650 Flattracker build.

Personally, I don't mind the look of a battery. I like easy access to the terminals (testing or jumping). I know most people like to try to hide them away, but they are an integral part of the motorcycle and I don't see any reason to hide them. I did clean off all the writing on the battery though. A quick spray of brake cleaner and all the writing wipes right off. Looks old fashioned when they are just black.
On the two I have done this way, I am using a very small battery because both bikes are kick start only. On the Smithers XS650 Bobber, it still has a starter motor (and a kick starter) and I am leaning towards keeping the electric starter. If I do, I will need a stock sized battery. The only good spot to mount one is down low right behind the engine. Again, I will probably mount it in a basket/bracket rather than try to hide it.
Have you ever seen the battery on my Chang Jiang? When the Changs went from 6 volt/kick start only to 12 volt with electric start, there was no room for the bigger battery in the old position. How did they mount it? They welded on a great big box on the side near the rear wheel. It sticks way out and is ugly as heck. Fortunately, with the sidecar on, you don't notice it too much, but it definitely looks like an afterthought. Some Chang Jiang owners move it inside the sidecar trunk, but I kinda like the way it just hangs there looking so ill conceived. If the Chang wasn't under a cover and a foot of snow, I'd snap a photo for you.
Peace & Grease, Dennis