Well, my first reaction was: "but they're not different!" Actually. there is a small difference, and I'll get to that later, but I suspect that a little explanation of Pronto Hex is in order. The main thing to understand is that Pronto Hex is not a code, but just measured times. So small differences aren't important.

The first 4 quads of the Hex mean:
0000 This is Raw format with modulated IR burst pairs
006D The frequency of modulation = 4,145,000/109=38KHz [6D in hexadecimal format is equivalent to 109 decimal]
0022 This hex signal has 34 (decimal) burst pairs that are sent once
0002 It has 2 burst pairs that are sent to repeat the signal

The remaining quads are the durations of the burst pairs, in units of the modulation period (1/38000 = 26microseconds). The on duration is first, followed by the off duration. So 0015 or 0016 (21 or 22 decimal) are almost the same time, differing by only about 5%.

Similarly 006C or 006D (108 or 109) are nearly the same frequency.  The actual NEC1 frequency would fall between these two integer numbers, so either is as correct as can be specified using the Pronto Hex format.  Moreover, 006C is the larger frequency, so the modulation period is slightly shorter, and the burst pairs need to have slightly larger numbers to get about the same duration.

So the only noticeable difference between post 11 and post 3 is the 5th from last quad 0699 versus 05ED. That is the so called lead out time-- the time between repeats of the signal. It is seldom very important. I didn't use the Yamaha converter; instead I used IrMaster.  MakeHex is also used frequently.  We know the specification for NEC1 signals, because NEC published them.  IrMaster gives 0699 using 006C as the frequency (lead out is thus 44mSec), while MakeHex give 0689 using 006D as the frequency (also 44mSec).  These are the correct durations according to the spec.

The Yamaha converter provides 40mSec of leadout, and is incorrect in that detail, but it will probably never affect anybody.

ETA: I had this backwards. 40mSec is the correct leadout and the Yamaha converter is correct, and the other two are off by 10%. Still not important. The actual NEC spec is 108mSec for total frame duration, and so the leadout will vary if the device and subdevice aren't binary complements.