If Darkness Falls only allows perk grease monkey 3 then that may be the issue as some of Manux's progressions require level 4 and 5 of grease monkey.
You could change this line to reflect 'level 3' in grease monkey to unlock the additional items for DF or alternately gate them behind Master Mechanic.
Code:
<append xpath="/progression/perks/perk[@name='perkGreaseMonkey']/effect_group/passive_effect[@level='[color="#00FFFF"][b]4,5[/b][/color]']/@tags">,manux_bigEngine,manux_vehicleBigWheels,vehicleGyroCopterAccessories</append>
Although the current progression file is gated for Vanilla play ... so would mess up again if you went back to vanilla at somepoint .
Edit : Although looking at manux's progression file you may need to change all 3 lines in progression.xml to give it a new structure to suit DF ....
Ragsy !!