Henry Ford payed to use a lot of other peoples patent rights as long as it didn't cost him an arm and a leg. He didn't like using Bendix brakes either due to costs but he used them on the Lincoln cars. He and Mallory were a lot alike and became good friends back in the late 20s. I'm sure they had agreements between them that were good for both parties and Mallory supplied Ford the parts he wanted, Ford name and all. Holley became the ignition supplier at the beginning of the 8BA era but this was after Henry Ford had passed and Henry II was running things.
Harvey Firestone was in the family and also close to Henry so Ford Motors used Firestone tires and many of those early ones had the Ford brand on them.
I'm not saying there wasn't any one else involved but Mallory was the original patent holder of the design that was used. Here is a link.
http://www.dragzine.com/news/video-a-brief-look-into-the-history-of-mallory-ignition/