This is also true, although Morrowind also does a pretty poor job with this at times. There are many instances where the game doesn't take multiple entry points into account but instead just starts a quest mid-way through. For instance, you may find a trinket in a cave and get a journal entry that says that you should bring it to a person you've never even talked to. This may occasionally be even game-breaking (going to Ilunibi too early) or cause you to miss big chunks of important content (talking to some of Caius' contacts before being ordered to do so by Caius). Still, even with all these problems I vastly prefer it to Skyrim's structure.
To be fair, this is annoying to deal with. Doable, yes, but you need to have a lot of extra scripting done to handle it, more so for more complex quests with multiple steps.
For example, when you pick up that quest item, you need to check if the player is already on the quest or not, and update the appropriate journal entry. Then you need to perhaps do different dialogue for the NPC or even different quest progression based on which quest state the player is in. Maybe it's as simple as adding an "I already have this item" line but it could potentially change the flow of the quest depending on how it is constructed (for instance, maybe the NPC is supposed to travel somewhere else while you are "out finding the item").
You can just take the Fallout approach of having no journal updates for anything and making the player keep track of it all mentally, but it doesn't really suit a game of such a large scale to do it that way.