You are correct - it did patch the original executable (and in the case of my situation, upgraded it from 1.0 to 1.2 in the process).. I think I had a crack for 1.2 on one of the many copiers of the days gone by - Probably on ProjectD, if I remember right. I could probably fudge my way through a manual install of all these things to get SimCity upgraded to 1.2 on an ADF, apply the patch for the graphics sets, then copy the floppy image with projectD to remove the copy protection, then install it to the hard drive... But the point was to bypass all this garbage and get a whdload that would just install it and patch properly up front.
Oh well... I can doo eet.