Dan, i think it needs to be clearer than that. A custom or bespoke service is one where a bat is made to your specification. This will generally be a more expensive service. A manufacturer of any size may provide it.
Speaking generally, a smaller company is likely to offer better customer service. That is always a good thing. A smaller company is not necessarily a custom company as they may only provide standard shapes.
There are also shades of grey, where a manufacturer may make "fab bat" and will adjust the shape of the standard product to meet your requirements. In my book this is still a custom bat.
The question of whether to choose a custom or an off the shelf should come down to a couple of factors. Do you understand enough about what you require in terms of weight, balance, middle position to request a custom or would you be better served visiting a cricket retailer to physically pick up a bunch of bats and decide that way? You may still get a smaller company's bat, but at least you'll know it suits you.