Not at all, it's there for a reason. Both ST and LT fuel trims are there to be used.
Think of a modern EFI stock car, they utilise both ST and LT as well.
Of course you want to have the injector data, coolant temp, fuel temp, fuel density, baro, air temp tables all correctly defined with fuel trims against them so your LT and ST aren't working hard to meet the AFR targets.
You'll also find that with bigger cams, you might need to target a bit richer than stoich as you'll find it will buckle.
I'll send some screen shots of how I set things up (once Lenovo the pricks send back my laptop, been 3x weeks to replace a mobo under warranty).