My '07 FLHTC has 1,000 miles and is currently undergoing a 120" build as I write this. Am I worried about the H-D powertrain warranty? No. Do I desire a dependable and durable powertrain that will offer significantly more performance? Absolutely. An intelligent performance build from a reputable shop will usually offer an equal or better level of dependability and durability than the EPA-compliant lean burn ECU settings of a near-stock warranty covered powertrain anyway. Performance builds typically address the inherrent vulnerabilities of the stock setup by including crankshaft timken bearing conversions, installation of better oil pumps, valvetrain components, the elimination of cam chains, tensioners, better ECU mapping/AFRs, etc... . I will retain the benefit of the warranty for any component, the stereo for example, that is not directly impacted by my modifications.
If you do not plan to include the stock powertrain vulnerabilities as part of your modification plan, the factory warranty should remain an important consideration for you.
Just my $.02.