Indirect injection diesel engines have been around since the beginning. There is no question that certain well designed IDI configurations produce little soot and smoke, as the violent mixing of the fuel air as it exits into the chamber does the trick.
The Lister CS (cold start) engines are an early example of this. The injector itself simply squirts a stream of fuel into the pre-chamber. Where it ignites and ejects itself into the main combustion chamber. The result is an engine that runs on nearly any fuel, and does so cleanly. But it only has one injector. IDI designs with multiple injection points can be both reasonably efficient and clean. We've known this forever.
But it's good to realize that nothing beats a well designed direct injection system for ultimate efficiency.
Opposed piston diesel engines, operating on a two stroke cycle, and utilizing multiple direct injectors seem to be the efficiency kings. With no energetic heat lost to a combustion chamber, and no friction producing wasted exhaust/intake stroke.
My point is this, the greater the exposed area in a combustion chamber, the greater the heat loss. Driving efficiency down. Sometimes substantially.