It’s kinda stuck as a consequence of year 3’s content being made as temporary content with sunsetting it all in mind. We only still have access to many of our current armor mods because sunsetting was such a bad idea that Bungie backed off.
Combat mods were a year 3 addition. All of the content in year 3 was meant to be vaulted and sunset. There were no plans to allow players to obtain these mods and items after year 3 ended. Bungie later decided to keep these mods in the game to make combat more engaging. They had no planned way to make these mods easily accessible. Thus we end up with the subpar vendor mod system that we currently have.
Is that more clear?
You misunderstood. That reason doesn’t explain why they choose not to replace the ad hoc system with something better. Especially as the list of mods continues to grow.