I worked on the movie and can tell you this first hand.
There were different versions of the same boots used yes, but not for the reasons you are mentioning.
The primary differences I noticed were the running boots which were modified for better grip and safety. All the boots Brandon wore were the same type of boot, but had different appearance due to whatever alterations were made.
After Brandon was killed and Dream Quest Images was employed to morph Brandon's face into the body double they were given a couple complete costumes for reference. The costume came with a couple different versions of boots, tops and jacket. All outfits were worn by Brandon and each was slightly different depending on use which lended to some obvious discrepancies.
The movie was made on a low budget so continuity sometimes took a back seat. On a side note. When a dream Quest was done with all the reference materials (wardrobe, storyboards, scripts, and photos) they tossed them in the dumpster. I fished them all out, kept one complete outfit and sold off the rest. The outfit is one of my best pieces.