You shouldn't have to do Compile 2. Note that your design is in a partition called Top automatically, so as long as you don't mind preserving the entire design(besides SignalTap, which is automatically not preserved), then just set that Top to Post-Fit.
When you do create a partition, your entire design has to be resynthesized and refit from scratch, so you can't preserve the stuff from Compile 1. Remember that a partition is synthesized independently of other partitions, and by doing so, it's placement info can be preserved. When you create a new partition in Compile 2, the partition information in Top changes too, so that has to be resynthesized and refit as well as your new partition. Skipping Compile 2 and just setting Top to Post-Fit will preserve everything and should work.
As for looking at pre-synthesis nodes, the answer is no, not if you want to preserve placement and routing. Those presynthesis nodes generally don't exist anymore. Think of a 2 input AND gate feeding a 3 input OR gate in your RTL. After synthesis, these may all be merged into a single LUT. If you want to tap the output of the AND gate, it doesn't exist anymore and the only way to get at it is to go back and resynthesize the design so the AND gate is the output of a LUT, but if you resynthesize then the node names change(and changes in one area of synthesis can affect other areas) so the post-fit information no longer applies.