If I give myself the following:

/give @s saddle{Enchantments:[{lvl:1,id:"minecraft:mending"}]}

and then right-click that saddle onto a horse (or any valid saddle mob, it's just easier to see on a horse) and check its inventory the saddle has lost the enchantment it had. Doing the same process but instead of right-clicking you ride the horse then open inventory and place it in manually it doesn't have this problem.