Dragging up a rather old thread here, but I've just been doing some further investigating into this, which I thought might be of interest.
It turns out not to be a difference due to patching the xbe. The XBE in question is older than the feb 2003 media check so didn't need patching. I extracted both the ISO created directly from the older ISO, and the ISO created from an extraction of the older ISO, and the contents were identical in a binary comparison.
Looking at the bytes in the ISOs around 00084000 that were different, as you say it seems these are the root directory entries. It looks to my eyes that the only difference is that the directory entries are in a different order. I'm not sure why the orders would be different, but maybe it's just one of those 'random' things that happens when you read a directory. Neither of the two ISOs appeared to have the directory entries in alphabetical order, out of interest.
It seems the two ISOs are not materially different, so it doesn't really matter. However, for obsessive people like myself ;-) it would be nice if ISOs created by both methods were binary identical (apart from the date stamp stuff at 0001001C, of course). For example, I'm glad to hear that you are intending to patch XBEs when converting ISOs on the fly, even though that wasn't the cause of the difference this time.