You can run the LDPs, CBE, and HE together w/o a tune, and you'll have no issues. (At one point in my mod progression, I had this exact combination before adding a JB4, which then eventually led to an Ecutek tune.) The stock ECM can compensate for the lower backpressure when the LDPs are installed. However, to optimize the air-fuel ratio (AFR) for the better exhaust scavenging with the LDPs, I'd recommend either the Burger Tuning JB4 or an Ecutek tune.Have you ran into any problems with your FI lower downpipes and exhaust? I have an 18' luxe with fast intentions catback and mishimoto heat exchanger but not sure if LDP will cause problems without a tune to keep my warranty.
As for standard or powertrain warranty applicability with LDPs installed, that will depend on the relationship with your dealership, and what specifically is the subject of the warranty claim.