Are there any difference between CTO version and the regular retail version MacBook?

There is NO difference between model 'on the shelf' and configure to order except models 'on the shelf' may be available to be delivered to you tomorrow.

Most Apple Resellers AND Apple-owned stores have VERY little "on the shelf" except the lowest-end models. Very little, if any, is available for pickup.

In major metropolitan areas such as major US cities, 'available inventory' is stocked collectively across ALL Apple stores in a geographic area, and yours may be delivered from a different store than the store you visited to place your order.

Almost All sales are of what you are calling 'Configure to Order', and everyone else calls "Regular". There is no 'warehouse' in the conventional sense of the word.

This is merely an extreme extension of 'Just in Time' manufacturing, where almost all models can be built to order and delivered to you worldwide in a few weeks time. In addition, Apple is also using collective 'stock' on the shelf at All nearby stores to fulfill deliveries in a narrow geographical area.

+1 to Grant Bennet-Alder's post. 👍🏽