Some initial structural thoughts:
Break the army into three sections from which the player can spend points. Tech Lord retinues, AM Defence Force, Planetary PDF. The Tech Lord section would be a minimum 1/3 point value (so 1000 points in a standard game) and the rest would be a maximum of 1/3 points.
All the cool Adeptus Mechanicus goodies would be available to the Tech Lord retinues. The better infantry and tanks would be part of the AM Defence Force and the grunts of the PDF would get the poorer quality tanks and few transport options.