vabsie, that's exactly how it works. You can turn most mapped entities on or off, on the main map. Regardless of whether they're turned on or not, they appear in the enroute features window if you clash with them. And regardless of your setting above which airspace is not shown, if you plot a route at that altitude, it IS shown.
bambuko, the new version that'll be released this week has the ability to export to .GPX but I've done it by referencing what's in the GPX reference only, so there's a chance it won't work. Feel free to private message me and I'll get an early version to you if you'd like to test it.
We also have fuel planning in this week's release.