Having spent a good amount of time on PBE testing supports with the new and improved gold flow, I can say a couple things. The gold difference that supports get is HUGE! Not small. I was amazed at how much stronger supports felt now, even though I was playing them exactly the same as I did on live. When I started to try and play differently according to the changes, they were even stronger.
If they kept the base damages and ratios at the same level as they do now, then AP Sona will do close to or more damage then the mages who are made for damage, while still playing as a support. That means your team can now have two super powerful apc's without having to make a sacrifice. They have to sacrifice nothing to gain tremendous power! Because now instead of being specifically good at support, growing/protecting the adc, proving benefits to your team, and making plays, or being a mage who does a lot of damage, Sona can do both at the same time while losing none. That means she can do what a full-on mage does, at the same time as being a full-on support.
To keep her from being that insanely powerful, they needed to reduce some of her base and ratios. But, because she has more gold then before, now she can afford regularly to get support items, supplemented by high ap items. Riot must balance for how possible a champ COULD be too.
If building Sona one way was too strong, they have to nerf Sona respectively. It's just how it has to be, because if one way is too strong, that's how people are going to build it, which in the end hurts their item choices even more than what you are saying. Why? Because, they will know that obviously they are OP when they build this way, and it is more effective than building the other way too. Also, they might have pressure from their team if their team sees them not building the OP way, increasing toxicity (potentially).
I know it might at first seem it sucks that Sona's numbers are being hit, but in reality it's a lot more complicated than that. I can tell you that in the end, you still have plenty of choice in buying support items, and Sona should still feel a great deal stronger.