Emanuel, I had the same problem (with the previous version), but I solved it simply by designing a two-layer board, and viewing the component-side tracks as jumper-wires. There is one caveat: jumper wires must be treated as components in the sense that they must start and end outside of any space occupied by the (real) components. So the procedure I recommend would be: start by autorouting, and if you are lucky all component-side tracks do not share space with any component. In that case you're done. Otherwise you can try shifting the vias to non-conflicting places. If that is not sufficient, design from scratch by hand, on the copper side only, as far as you can go. Then add tracks containing appropriate vias to complete the design. Try to minimize the amount of jumper wires. In my experience this always works.
regards, PvE
