So I get why Riot put Magical Footwear and Perfect Timing on the same line.

Riot wants players to make 'meaningful decisions'. Riot doesn't want you to be able to run a certain Rune Page and start the game with 950g already in the bank.

But why did Hextech Flashtraption get put on the same line?

Champions like Skarner and Volibear that this 'rule bending' Rune Tree was made to help end up being the worst-affected Champions from this change.

Riot COULD have nerfed the tree for ADCs and Mages who naturally buy Boots and Hourglass/GA and left a reasonably decent path available to champions who need it.

And, for that matter, I think every Mage at Pro Level will just start taking Minion Dematerialiser now out of obligation. At first people were sacrificing something to get it and it actually had some cool interactions where you could hard shove with the extra % damage to minions and roam, but now it's up against two fairly irrelevant Runes (Biscuit Delivery & Future's Market) so people will HAVE to take it so that they can match the enemy's wave clear.