The iron being removed isn't from the "tooling bits", it's native in the steel itself (of the blade).
Passivation reacts with this surface level of iron and removes it leaving behind a passive surface of Chromium oxides which resist corrosion much better than free iron, hence the reason it's done.
If the surface of the steel becomes damaged, you will have to passivate again to deal with the iron now exposed in the damaged area.
Most modern tooling bits used these days to mill the steel are sintered carbide, not steel, which have extreme wear resistance and really won't be leaving any iron in the object being machined anyways. Even if it was HSS like a common drill bit, the amount of iron it may leave on a knife is negligible and only on the surface if it were to break off (unless you crash the machine and really bury that sucker in your work piece, then it can really be embedded in there! Lol). The amount exposed in the freshly machined knife blade is a part of the blade steel itself and is far greater than anything coming out of the machining cutters.