This question can't be answered in general because it's totally hardware and OS dependent. However a typical answer is that the initially loaded program can be compiled as you say: Because the VM hardware gives each program its own address space, all addresses can be fixed when the program is linked. No recalculation of addresses at load time is needed.
Things get much more interesting with dynamically loaded libraries because two used by the same initially loaded program might be compiled with the same base address, so their address spaces overlap.
One approach to this problem is to require Position Independent Code in DLLs. In such code all addresses are relative to the code itself. Jumps are usually relative to the PC (though a code segment register can also be used). Data are also relative to some data segment or base register. To choose the runtime location, the PIC code itself needs no change. Only the segment or base register(s) need(s) be set whenever in the prelude of every DLL routine.
PIC tends to be a bit slower than position dependent code because there's additional address arithmetic and the PC and/or base registers can bottleneck the processor's instruction pipeline.
So the other approach is for the loader to rebase the DLL code when necessary to eliminate address space overlaps. For this the DLL must include a table of all the absolute addresses in the code. The loader computes an offset between the assumed code and data base addresses and actual, then traverses the table, adding the offset to each absolute address as the program is copied into VM.
DLLs also have a table of entry points so that the calling program knows where the library procedures start. These must be adjusted as well.
Rebasing is not great for performance either. It slows down loading. Moreover, it defeats sharing of DLL code. You need at least one copy per rebase offset.
For these reasons, DLLs that are part of Windows are deliberately compiled with non-overlapping VM address spaces. This speeds loading and allows sharing. If you ever notice that a 3rd party DLL crunches the disk and loads slowly, while MS DLLs like the C runtime library load quickly, you are seeing the effects of rebasing in Windows.
You can infer more about this topic by reading about object file formats. Here is one example.