You are absolutely correct that a custom rod will not offer more performance than a factory rod of the same blank model simip0ly because a blank performs in a given way regardless of whether assembled by the factory or a custom builder. However, a factory will not let you have difference thread colors, won't put feather inlays on a rod, won't let you have a differently shaped grip, won't put on a different reel seat or use a different wood insert in the reel seat, won't put oversize guides on the rod for you, won't put your name in thread on the rod, and won't put different guides on the rods for you. For example, Sage will not put gold thread, Fuji SIC strippers, oversize TiCH snake guides, make the grip larger diameter (or smaller diameter), or an engraved REC reel seat on the rod for you. To get those, you either have to built it yourself from the Sage blank or have a custom rod builder build it and put this things on it for you and be prepared to pay more because the reel seat and TiCH guides cost more.
Some rod manufacturers (like Meiser and Orvis) will do these things for you as a non-refundable special order; but the price might very well be than the standard factory rod because the components could be more expensive and the time it takes to add feather inlays or thread weaves.
That said, there blanks on the market that are not available as finished rods, and the only way to get a rod made on one of them is by either building it yourself or having it built for you.
It still comes down to whether 1) you want to have different size grips, different reel seats, different strippers and snake guides, different color threads, etc. than the factory puts on the rod; or 2) you want a thread weave, feather inlays, or your name in thread on the rod; or 3) if you want to save a little money by building it yourself.
As to whether a rod is an investment or not, I submit that a rod is never an investment (unless you get a bamboo from one of the high end makers and never fish it). Instead it is a fishing tool that you should buy because it fits the flies sizes you are going to fish, fits the fish you are going fishing for, suits your casting style, and you are happy with its cosmetics. Any rod, other than the high-end bamboos, are going to depreciate as soon as you take them home from the store. This is true for factory rods and custom rods. The big reason shops can get more for a factory rod than a custom is that the manufacturer's warrantee applies to the whole factory rod; but only to the blank of the custom rod.
For example, you buy a Sage 9141-4 used and break the tip section, Sage will replace it for you at no charge. However, if you buy a used custom built on the Sage 9141-4 blank and break the tip section, Sage might replace the tip section of the blank; but Sage will not give you a new complete tip section. You will have to buy the guides and pay someone to wrap the guides on the blank and finish the thread wraps with epoxy. Thus, it will cost you money if you break the one custom built on the Sage 9141-4 blank to have it fixed, and it will cost you nothing if you break the Sage factory built 9141-4.