But that's all besides the point - why would Bioware charge more to the consumer for an end product that costs them less?
Because people will pay it. That's all that ever matters. Prices are set at the level the market will bear.
Also, it's possible that there are relevant demographic differences between the two pools of consumers. People who like boxed copies might be less wealthy (this makes sense, actually, as poorer less educated people are less likely to have access to high speed Internet). And as long as the price difference isn't great enough to create a reselling market (in the way that tobacco taxes sometimes do), there's little risk that EA is leaving money on the table.
Also, maybe there are costs we don't see. Maybe digital purchasers tend to place a greater burden on support services. Much business software these days seems designed not to be better, but to reduce the number of times people will call support. There could be a similar motive here.
I get the argument "they can, so they will" from a free-market mindset, but not from a logical one. Unless politics between retailers comes into play, where there is the decision to promote retail sales because companies like GameStop want people to come in and also buy accessories or the extra DLC package or something.
Given EA's objective here, the free-market mindset is the logical one.
Another thing occurs to me. Brick & Mortar game stores are struggling. Given that some consumers do seem to insist on buying physical copies, EA needs stores to survive. Theg could well be trying to prop up the sector to avoid losing that segment of their playerbase.