Back before the airlines decided they wanted to court bicycle riders, I bought a very nice custom bike with S&S couplers so I could fly inexpensively with it. It's a lovely bike; tricked out with just what I wanted. Worth the investment? I don't know; I doubt I saved enough to cover the price in lower baggage fees. However, I never had to worry about finding a decent bike to rent, and I took it on a few trips where I wouldn't have traveled with it otherwise. It's the lightest, sportiest bike I own. I'm not giving it up.
On the other hand, you can buy a very nice stock bike and have it fit to you rather inexpensively (compared to custom). Pay for a bike fit, get a new stem, put on your favorite saddle, and fit-wise and comfort-wise, most people end up right where you'd be with a custom bike.
On the other other hand, maybe you'd rather have a specific crank, gearing, shifters, braking system, and refitting a new bike with your favorites could significantly increase the cost.
My recommendation: buy a high end production bike unless there's some reason not to. It could be fit (are you built like a gorilla, or Andre the Giant?); it might be that you've always wanted some special bling, whether it's Phil Wood headset and bottom bracket or 180 mm disc brakes on a road bike or your name etched into the titanium top tube. Bottom line, only you can decide if it's worth it.