That is not how it works. Y is always relative to map base not the object over it.
To build stuff easily, you need a completely flat map, where the absolute Y = relative Y.
Also, the LOC command gives you absolute Y. So you stand on the ground and read 80 for Y for example. Then put down something there. If you type 80 for the Y coordinate then the object will be 80 feet OVER the ground because it is relative to the ground elevation.
There is a little hack to work around it but it still needs double work to counter the un-even terrain while building stuff.