Is there any disadvantage in buying a customized macbook pro vs stock config?

There is a major advantage to custom ordering your new MacBook Pro and that is for things like memory and storage. The newest models do not sport some user-upgradeable features. If, for example, you got yours at the Apple Store with 8 GB of RAM, and then, decided that you want to have 16 GBs, you may not be able to do so.

We can't discuss what we think is Apples motivation behind their pricing as it's against the TOS of this forum. Most if not all computer makers offer a base model with upgrades, and not a upgrade model with downgrades. The same could be said for car makers, it's a common practice.

However I have also been advised by some of macboook owners that it is always better to go with stock configuration as customization of hardware like mac is not advisable and won't have the same Quality Checks a stock machine goes under.

that advice is out-of-date.

It assumes that some options were plugged into sockets or slots in a low-tech "factory" and there was no additional quality-control after they were added.

Today, EVERY item listed as "available options" is soldered to the mainboard, and undergoes exactly the same quality checks in the same factory where it is made.

When you see "available" it does NOT mean you can upgrade at a later date. All options are now FIXED at the time of purchase, and manufactured to those specifications, and NOT Upgradeable.

There are no items in sockets on the latest battery-powered, portable notebook computers from Apple.

--------

The disadvantage of ordering with options is that you can't walk into a store and walk out with your new Mac today.

There are no disadvantages to ordering a customized version from Apple that I've ever experienced or heard of.