It mostly has to do with the 40-man roster. Putting a player on the 60-day IL frees up a 40-man roster spot. Some MLB teams don’t need this roster spot and don’t want to put someone on their 40-man because it affects service time, how much you have to pay a player, etc.
From the MLB rules on the 60-day IL (relaying this from @joecatz)
A player who is placed on the MLB 60-day Injured List during Spring Training must spend at least the first 60 days of the MLB regular season on the Injured List (the player cannot be reinstated any earlier than the 61st day of the MLB regular season).