This is not really surprising. Many business and entry level users don't need more than 16Gb and it keeps costs down. One thing that irks me though is that they do not include a 32Gb version. By now it should cost the same as a 16Gb chip 4 years ago, so they could (if they would be willing to take the profitability hit) make the base model 16Gb 50$ cheaper and the 32Gb model at the current entry price. But I guess Apple is not willing to do that. A pity.
You hit the nail on the head-- the 16GB/$299 is the Corporate model (my company has a $299 limit on company provided phones, for example). But Apple is addressing your other concern by increasing the amount of storage in the $100 uptick model, which is the one aimed at consumers. There is no way Apple is making the entry level model of the flagship phone cheaper, as corporate limits change very slowly. Cutting the entry price is just leaving money on the table.