I don't look at one as "better" than the other, they are different and the differences are what must be studied. To paraphrase Bowen, a Ruger can never be rebuilt as tight as a Freedom Arms is from the start. Because they are built right from the start. They are built as precisely as possible and like any precision instrument, they shoot like it. That said, they leave me completely cold. To me, FA's have all the appeal of a precision surgical instrument. No soul, if that's what you want to call it. An FA can be made in any material and with any finish you like as long as it's brushed (or beadblasted as with the Field Grade) stainless steel. Options are limited and if you can find what you want within their parameters and price range, you can do no better.
A custom can be anything you want it to be. As plain or fancy as you like. As "standard" or accurate as you're willing to pay for. A full custom linebored Ruger will be every bit as accurate as an FA but it will also cost more. They can be fitted with the sights of your choosing. They can be finished in hot salt blue, rust blue, charcoal blue, nitre blue, color case hardening, any of the high tech coatings, hard chrome or nickel plated, etc.. The options are almost limitless. Barrels can be round, octagon or ovate. They can be retrofitted with DA barrels such as those from Colt's or S&W's. Top straps can be welded up and reshaped in the old M&P style, dovetailed Single Six or Colt SAA. Grip frames can be swapped, welded up and/or reshaped. Same for hammers & triggers. Like I said, anything you want.
BFR's are good guns, somewhere between FA and Ruger for quality. Perhaps most comparable to a mild custom Ruger. Lock is tighter, fit & finish is better and they are usually more accurate. Like FA's they only come in stainless steel and there are no options for swapping the grip frame but they can be reshaped. Contrary to the ramblings of a crazy old man, they are not better guns than FA and I'll gladly pay $100 for every half inch, five-shot group at 100yds. Problem with BFRSHOOTER is that he makes broadly sweeping conclusions based on singular, statistically insignificant events. Even his buddies at the treehouse club agree on that point. Sorry but two shots on a shotshell hull out of 20shots fired at 100yds don't add up to a half inch group.
Recoil is highly subjective and what you have to do is find what works for you. I'd suggest doing this before paying thousands of dollars for a custom or FA. Some folks like the FA, some prefer the Ruger Bisley, some like both. Best to figure this out before committing.
To me, gunmakers that use other people's actions as a basis for customization are just that: Customizers; not true custom gun makers.
Most people would strongly disagree with that. If you think that R.F. Sedgley was just a "customizer" because he started with a Colt Flat-top Target to build the famous Keith #5, or Bowen using a USFA Flat-top to build his replica, then your compass is broken.