The rules do provide for the averaging of D6 across commands in regular armies. This would split the PIP score as evenly as possible, but rather than 'rounding up' the additional points would be allocated to commands according to a priority system, e.g. right flank, then centre, or right flank then left flank. There is of course a probability curve of scores with this system which one wouldn't get with a D10 or D12.
2D6 would produce a range of 2 to 12 with 7 as the most frequent result 6/36; which would be interpreted as a PIP 'spread' of 3,2,2, with 3,3,2 or 2,2,2 next most frequent, between them accounting for 16/36 rolls. The probability of 12 would of course be 1/36, of 11 (or 4,4,3) 2/36, of 10 (or 4,3,3) 3/36. As you note on a 2D6 chart you can't include all the outcomes that you might get from rolling 3D4, but it is possible to get most on such a chart. for example nine can be scored by 5 + 4 or 6 + 3, and nine could be allocated as PIP of 4 4 1 or 4 3 2 or 3 3 3. So, does one eliminate the most average result 3 3 3 or the most extreme 4 4 1, or allocate 4 3 2 to all ?
Given that the highest number of PIP that can be allocated to a command is 4 and each must be allocated a minimum of one, provided commands are given priority, as above, they detail of the allocation could be left to the player. For example a throw of 7, obviously the most probable score, would give the player a choice between 4 2 and 1, 3 3 and 1, or 3 2 and 2. The higher number in each case allocated to the top priority command and the lower to the lowest priority command.
One question is what to do if the 2D6 score is 2. One option is to allow the points to be used in any command, but only for defensive actions, e.g. for an element to turn to face a threat or withdraw from a threat, unless perhaps an attack led personally by a general. The other option is simply to re-roll.
I should probably try each. I have tried one re-fight of Paraitakene, using 2D6 and 'averaging', which went well. Markedly better for Antigonos than Eumenes . . .