How much R&D and trial and error goes into "first"?
There's a huge number of variables for stuff like this. A single change often has unexpected results and/or consequences.
The paper you linked to uses a test engine with 83mm bore, vs 94mm for 1HD-T. That alone changes things. A combustion chamber design that works for 83mm, may be way off the mark for 94mm. They discussed changes in bowl diameter of a few mm making big differences, but made no mention of bowl shapes.
They used injection pressures of 130Mpa, ~19000psi vs ~2200psi for 1HD-T.
There's also ythings like injector placement, nozzle orifice size, injection spray angle, injection timing and duration, valve placement, port angle. All play a part.
I'm interested to see what other info you can dig up