The rate of a skill in the Mission planner isn't modified by the presence of Customized equipment. I got a piece of kit up to lvl 4, so it should boost speed by +4% if I understand the writeup correctly, but the applicable skill speed in Mission planning is unadjusted, staying the same whether I have the customized item equiped or not.
Viewing post in Update 1.3.3 - Plans and Fury comments
It should be a rate change of +.08 at level 4 (.01->.02->.04->.08) which doesn't quite map to an 8% bonus to speed but should be close if it's your only rate change bonus (normal completion time / (1+rate bonus) = final completion time). Either way there should be some change to rate though. I'll dig in, likely something isn't wired up fully.