An OPL3 has only 36 operators so theoretically it could ever have 36/4 or 9 channels in 4-op mode, not 12.
This is all speculation, but as it had to be OPL2 compatible, they made it look almost like dual OPL2, register-wise.
As the first half is completely OPL2 compatible, which had to be able to divide 9 2-op channels into 6 2-op channels and 6 rhythm operators, it was most likely easier to just be able to leave the rhythm operators alone so only the 6 standard 2-op channels were modified so that they can be set into 3 4-op channels.
Then if you just use copy-paste this to double the chip channels, but leave out the rhythm mode from the clone, you have an OPL3.
*12 2-op channels which can be comined freely up to 6 4-op channels
*3 2-op channels which can be set into rhythm mode
*3 2-op channels that are fixed
But hey, since this is an emulator, you have no hardware limits, and you are free to build an OPL3 emulator/synthesizer in steroids, like having any amount of simulated chips for any amount of 4-op channels.