BGL2XML should work fine. I guess you don't have an current version because it's should be able to decompile exclusions. Missing exclusions are the cause of default scenery taking over.
However, I don't think there are any problems editing with ADE or AFX, as long as you use current versions (ADE is updated very often) and, an easier solution might be working with ADE, and use the option to keep the XML source, so you can check if all parameters are correct (exclusions zones and the "DeleteApproaches=False" we usually use).
It's not that ADE does anything magical: it STILL compiles the XML source it produces with BGLCOMP, and the option to keep the XML source is only there to prevent it from *deleting* it after the .BGL is ready.
AFX might be a bit tricky, because it doesn't work with an intermediate XML and doesn't use BGLCOMP: it compiles directly to binary format so, if you use AFX, you usually have to decompile it with BGL2XML and the recompile it with BGLCOMP.
But in any case, the only reason to do this, is to be sure exclusion zones are preserved and the "DeleteApproaches=False" is preserved too. If you check they are preserved using just the editors (in their most current version), you don't have to do all this decompiling and recompiling.
Just keep in mind that, whenever you reinstall a scenery or the Stand-Alone Addon Manager, your modified files will be renamed and the original file that comes with the scenery will be restored.