Out of interest, when do you have the cost of the rebuild written off in your calculations - many PC building enthusiasts enjoy a "Ship of Theseus" experience with their equipment; replacing parts piecemeal as and when they deem it necessary.
With the prebuild OEMs their unifying warranty is indeed a plus, but it becomes a curse when it's finished - it is frequently not possible to replace failed parts on these systems at reasonable expense, due to customised model-specific parts (non-standard motherboard shapes, non-ATX power supplies, weird CPU Cooler mounting hardware) - in the gaming world this is alive and well today in Dell's Alienware and own brand gaming PCs, and in the workstation world, basically anything Dual Socket is frequently super custom.
The custom build may have more utility after one of it's standardised components fails out of warranty, as this standardisation allows for a choice of replacement (either in matters of cost or performance). If the prebuild fails out of warranty you may have some eWaste on your hands if a non standardised component fails.