you are correct the engine was build without the spring and stud. The factory must have had some tool to tension the timing belt so there was no need for them. But to replace the belt you do need the spring and stud to prperly tension the belt.
now to me it seems to make sense that the belt might stretch some. I haven't heard anything from mine since I replaced the timing belt. I do know mine was hitting the cover for the longest time and the belt only showed a little wear from it.
I would say either get the revised cover, which is a bit taller, or use washers to raise you current cover and that will remove the noise.
you could also just remove the cover but I don't personally like that idea