I think there are a lot of things to consider.
First off, there are some brilliant bespoke makers on this site, and I don't think they could be classed as selling 'out of a car boot.'
Some of these guys offer a high level of involvement, from selecting the cleft and input during the making process etc. This can obviously be important in respect of pick up, shape, and finished, fully dressed weight. Obviously this is most effective if it is done during a visit to the maker's premises. And under these circumstances there is no excuse for you walking out of the door with a bat that is not exactly as you specified, as you have been part of the process.
I will admit that I haven't been part of such a process - maybe my day will come.
There is also the option of more remote involvement - giving the maker your specs and trusting to his judgement to produce exactly what you want. From what I gather, quite a few makers will contact buyers during the process with updates in respect of how the bat is coming along. Maybe with questions like: 'How important is the finished weight to you? The way this cleft is going I might not be able to give you the spine height and edge size that you requested at the weight you want. If you do want me to lose some weight, where do you prefer me to take it from?'
I have seen guys on this site post pics of some very good looking bats, but with the rider: 'I asked for weight X and what arrived was weight Y.'
It could have been that the bat was the stated weight 'undressed' but I would have thought that this would have been discussed before the bat was made.
In the case of the retailer, and ignoring his overheads for running premises, holding a good level of stock etc. What you get when you visit, is the opportunity to pick up and test a number of bats, before either selecting one or not bothering to buy anything. That opportunity in itself has value and is surely worth paying for.
What I'm trying to say is that everyone brings something to the party.
Obviously you wouldn't expect the same level of service at say Sports Direct, as you would from any of the retail guys on this site. But you cut your cloth accordingly.