Most of my layouts have been portable, modular or temporary in both O and S gauge. When temporary, I try to cover the table or plywood surface with something like foam board, carpet or even cloth to sort of even out the bumps, and I have found both types of track to be fairly forgiving with small changes in elevation.
You didn't say how the rest of you layout surface is covered or accessible, but it I am assuming that there has to be a clean break between the layout now and the new section with no ability to transition or countersink the new piece into the table surface or sub roadbed.
I suspect that old school tubular could span the intersection of an actual change in the layout surface between its widely spaced ties and minimize the "teeter totter" effect better than a solid section of FasTrack. FasTrack also could leave a slight gap between the roadbed and the table, which would affect the "realism" of the integrated ties and roadbed.
At the same time, I would try not to have the abrupt height change occur too near the connection between the two sections of track to minimize the chance of a sharp kink.
Finally, as you mentioned, whatever you can do on the layout itself to shim or otherwise ease the transition wil help.
Good luck with your project.
Alan
