Maybe it's an issue of perception. Maybe the book itself implies who will be the one to decide the rules within are included. If the players get to decide which rules are used and which ones aren't (by not choosing feats for their characters, or not choosing to play a variant human, etc.), then I'd expect all optional rules to be printed in the Player's Handbook. But they're not.
And if the DM is the one who decides which rules are included and which ones aren't, then those rules should be printed in the Dungeon Master's Guide, then I'd expect all optional rules to be printed in the Dungeon Master's Guide. But they're not.
Instead, we currently have some optional rules in the PHB and others in the DMG, and it causes a lot of unnecessary conflict at my table. The players aren't clear about which "options" are actually options, and the DM--that's me!--has to endure a lot of push-back and arguments from the players whenever he wants to add stuff from the DMG (or remove stuff from the PHB).
All I ask is that they make a clear distinction. Whether they are in the Dungeon Master's Guide or the Player's Handbook, I hope they put them in their own chapter named "Optional Rules: Check With Your DM First!" I think it would make things a lot easier, especially for newcomers to the game. Having them sprinkled around in several places, and in different books, isn't as helpful as it could be.