If the space marine weapons, equipment( jump packs) and some vehicles( droppod, hover bike) are supposed for their superhuman physiology and reflexes, how there are STC for all of that made in dark age?
There aren't. Any STCs of bolters and Power Armour were made after dark age, during Emprahs times. Mechanicus do know how to make and copy STCs, they lack the knowledge of what to put inside them (They lost more during HH than anytime before, also Emperor was around with all his wits). As for the "Dark Age Of Technology" vehicles and stuff, Mechanicus have changed them to bear Imperial marks and stuff, since they can do it too, they just don't exactly like making big modifications because it's very easy to break shit if you don't have any idea how it works. Also they're too damn religious.
I think the Emperor modded them.
Which doesn't make an amazing amount of sense.
Back during Unification Wars, there were those proto-Space Marines called Thunder Warriors which used some kind of early power armour and bolters, like some other techno-barbarians. While those things could be STCs, it's more than likely there was no way of using STCs on Terra back then, and even if there were, nobody had any idea. After Emperor hooked up with Mechanicus and then made up first Power Armour marks (the fact that they were upgraded through the existence of IotM should hint they're not old STCs) with their help.
So while Space Marine Power Armour and Bolters do use parts of old STCs, they are one of few things that Imperium actually did themselves.