A lot of it depends on how hard you and/or your boot fitter are willing to work on modifications like those people have talked about here.
I'd say that if you are happy with something you find in stock at a pro shop, go for it. The decision is harder to make if nothing in stock fits. Especially for guys, since most pro shops don't stock a lot of guy's sizes. But for both, it's not at all uncommon for people to spend a dozen or more hours driving around to pro shops to see if they can find something that fits, or comes close enough for you to order a slightly different size of the same brand and model.
Heat molding complicates the issue. You can't expect a fitter to heat mold the boot to you before you buy (assuming it is a model that does heat mold), and without that, it might be hard to decide. Heat molding probably may not fix things that hurt a fair bit, or toes that hurt at all (because there is very little molding at the bottom of the boot), but it may fix something that is just a little loose or tight at the top.
It also depends on the type of boot and the pro shop. If something is a little tight at the bottom, you can often get extra space by removing the insole, and/or replacing it with something very thin. But some insoles are glued in, and the pro shop may not let you remove it.
Are you new to skating? If so, you may want to try to make do with stock boots for a while, because you may not know yet how much support you will need. Unless it hurts.
I know this sounds ridiculous, but a lot of skaters start with stock boots, and are unsatisfied, and decide to buy a pair of custom boots too. One advantage of custom boots, is that most of the custom boot makers (check with yours! - the manufacturer, not the pro shop) will buy the boots back from you at a full refund it you aren't happy with the fit. You can ask, but they probably won't do that if you buy stock. But your pro shop might offer such a fit warranty anyway.
Anyway, stock vs custom is a decision I would hope a really good fitter would help you make. Are there any within a day's drive or so? If you are still near Fort Lauderdale, there is supposed to be someone really good in charge of a pro shop in Coral Gables. I forget the name: he used to work in Virginia, at Ashburn and Kettlers. I know it sounds insane to ask a merchant, "Should I spend more?", but honesty is one of the characteristics you expect out of top people.
If you don't find a pair that fits perfectly in stock, going to a really good fitter seems like an expensive luxury - you don't get discount prices - but IMO it's one of the best investments you can make as a skater.