The bolt on the top of the strut changes height depending on if the car is on the ground or lifted of the wheels.
Car on jacks:

 

 

Car on the ground:

 

 

The bolt protrudes approximately 1mm further up if the car is supporting itself. I even took the strut out and rebuilt it and checked all torqued bolts, all is as it should be as far as i can tell.

This is normal as when you jack the bodywork up the suspension just hangs down and the spring has expanded, when you put the car onto the ground the wkole weight pushes the spring and slightly compresses the spring and the top rubber mount allowing the strut rod to go a little higher, if it was moving 10mm or more then i would worry but this is fine , you can check the top mount buy jacking up the car and supporting the weight of the car then put the jack under the suspension arm near the bottom ball joint and slightly jack up the strut just enough to take the weight of the strut and then you can push/pull the strut end from the top and see if you have any movement in the bush,these can be replaced if needed, on some cars you needed to clamp the coil spring before jackinng upthe car by the bodywork i would not worry about this seems normal to me just perhaps uou have not noticed it before 

Thank you so much for the reply, it got me really worried since i can also hear a subtle thump noise when i drive over potholes and the like. I pulled the suspension again and had someone that's a hobby mechanic to look over it. All is as it should and no play in anything we could see or feel. I guess the thump sound is just from the new struts being stiffer than the old ones that had close to 200km on them.