The baseboard radiator is supposed to rest upon the "Finished Floor". However, if there is rug then it would rest on the subfloor and the rug atop the subfloor as well.
The endcaps should cover. Note. If you have hardwood and the radiators are off the hardwood , you will see the copper pipe even if the radiator is above by 1/2" or more.
You have a choice... either have the contractor lower the radiators or give it 2 weeks and you will forget all about it.
It's amazing the things we notice and then after a little bit of time wont even think twice about