I compiled PK3DS from GitHub, and with the feature I requested and at least for OR/AS (6 pokemon in important battles) all extra pokemon implemented are level 1 for all battles they are in for:
http://puu.sh/lvKCA/4887f562fe.png Original pokemon with level scaling randomizer option
http://puu.sh/lvKCY/1894968be4.png Additional pokemon that were added with the important battle 6 pokemon feature.
Small oversight, I guess? Even with Level scaling by 50% checked they still remain level 1, and with the important 6 pokemon unchecked. basically, same result no matter what. I also figure it would defeat the point as well if you had to go back and level scale them after you randomize + level scale, as it'd scale every other pokemon up again.
So, having it also include the six pokemon in a base min/max range (1-5 sounds good?) of the levels of the last pokemon on the original team would be fine on top of what's already implemented? (i.e lv.51 orginal pokemon, 53 original poke, 55 randomized poke, 54, 56, 57, 54) and so on.