I am for giving factories 100 storage, commanders 500 and dedicated storage 500/1000 (with cost/hp increased a bit). Mostly for convenience reasons, shrinking commander blow and because it makes sense.
I don't see why it violates a quants rule. If you want a tool dedicated for the job, you use it (anti air), but it does not hurt that there are other units that can do the job, just poorly and not as effective (other units).
I think that even if factories had little storage, in all situations you currently need a storage you would still build a storage, just maybe not so urgently. Tying up storage with units is a bad idea though.
Now is not a good time for changes, but I'd reconsider this in the future.