What is Riot's answer to the loss of player/role customization option with the new Rune system?

I wrote this in answer to another post, but I feel like I should open up a discussion as most of the issues dealing with the new rune system seem to be based on fear of power balance. This post is more of customization loss.

My concerns are what we are losing rather than what we are gaining.

I understand that the runes are an extension of the keystone changes that were an introduction. So we are getting the next step in keystones and masteries evolution. But we are calling them runes and removing the rune system. So what are we losing?:

Stat customization - I've always liked how I can modify my runes to suit the role I wish to play. For example, I like to play jungle, but some champs do not work as well there early game. So I can add runes to add attack speed for clears as an example. Or I can add armor for a little early tankiness. Another example is if I want to forego any defense at mid and make a glass cannon. In this example I am taking a large risk, but it is MY risk because I could customize for that accordingly.

Riot's answer to rune stat removal - It's my understanding that Riot will be looking at changing base stats to accommodate the loss of stat customization. I feel this removes the customization options from players, and puts them directly in the hands of Riot. Basically, it sounds like Riot is saying "we like champs to play roles and styles the way we intended, and any customization that deviates from this intention will either be removed, or limited."

The problem with masteries is the tree system locks you into certain paths. The benefit of runes is that you can basically choose to invest in a stat in any given location. You get more benefit of course from investing in a given stat in marks, over glyphs, but you could choose the glyphs because marks give a better efficiency in a different stat. There are limitations, but the customization possibilities are still there. My suggestion/understanding of Riot's answer to this may be entirely incorrect, but what IS Riot's answer to the loss of customization?

TL;DR New runes are en extension of Masteries and keystones which are path based and have limited customization. Removal of old runes removes a level of player customization, while adjustment to base stats are in Riot's hands, not the player. Where do players get compensation in customization loss?