I bought a couple sets of strut extenders from Boondox (in Michigan). Went to screw them onto my Gabriel struts and had the same problem too. My heart sunk. I thought all that work and now I'd have to reassemble to stock and think of something else.
However... what ended up working for me was an air dremmel with a course scuff pad mounted on it. Hang on to the strut tightly and move it around the top of the strut shaft just below the threads and buff the shaft down. You might want to run a nut down to the bottom of the threads to protect them, although the extenders don't screw downall the way. After a few minutes of buffing while rotating the strut shaft trial fit the extender for clearance. After you gain the needed clearance, coat the shaft with a light coat of grease (to prevent rust bond) and tighten. Be careful cause the shaft will be more than warm to the touch! The air dremmel removes just a little material at a time. In fact, it "buffs" the metal off. Within five minutes, you should be able to buff off the clearance obstruction. You could also buff off the inside of the extender, but my thought was you would be removing metal from a fairly thin wall anyway, so i took it off the shaft.
BLUF: The extenders need engineered with more inside diamater clearance. I'm talking X amount of thousandth of more diameter.