How 'bout this. Work in the KGC is compartmentalized. Consistently. Jesse James has been referred to as the 'comptroller'. Suppose there is a small collection of 'treasure site pickers and designers'. They figure the site out, leave signs like tree carvings or tree manipulations for manual labor end of things that comes through at a later date.
Site choice is a huge consideration for whatever the end goals may have been, as security and recoverability are paramount considerations. On top of that, site preparation takes time and coordination. Jesse and the Boys are on the run, having just robbed a train, bank, etc., and now a posse is on their trail. There wouldn't be time to think out and lay out a site afterwards. You could even compartmentalize further, have the labor boys dig multiple holes, and move on to the next site, while another group places the treasure, while yet the original site designer (who could know where the caches are located, could come back through and change the signs, to keep the location info limited an unable to being passed on to a future person from one of the labor party's son, grandson, friend, etc., being given 'The Key' to decipher the treasure site.
Things like that can explain all of those 'deer hunters' of the 30's that stumbled upon a cache, but could never find their way back. Cache owners would PROACTIVELY guard their locations from the future desires of those (like low on the totem pole manual labor) that may have helped place them - can't just slaughter them and kick them in a hole like the Spanish have been purported to do with some Native Americans.
Trees would not have been used as a long-term site marker. But for a short term, in the manner I described ...