It's a guitar assembly process. They aren't building guitars to order like EBMM or to an extent the Fender custom shop, rather just assembling guitars from already available parts. You can choose any of the available standard color body, combine with available standard neck offerings and pickguard option and you have a "custom" mod guitar. There is nothing wrong with this, but this was the way you have ordered EBMM for years except BP and Co don't make or stock standing parts so everything is built to order.
Like Stratty said ... this is already how you order an EBMM - pick the available options and there you go.
To the larger issue of a custom shop (or a 'mod shop' with more options), the real question is whether that approach is profitable. BP has said on many occasions that it's not worth doing for them, as they only have so much production capacity and most of their sales are through the dealer network (that favors particular items).
im simply fancying the ease of ordering using the already available "stock" parts bins available for the 4 models they are offering. It's a good example of slick marketing meets ease of ordering. Not any different that the model used on your average car OEM website where you can "build your own" and see it on the page, walk through the options... And in Fender's case... Click so they can collect your $$! This puts value at customer and revenue at the manufacturer. Simple business principals.
I am not trying to suggest a custom shop. I am trying to suggest an interesting way to route interest/orders to EBMM!