I don't think the 3 will have the margins for that in the base model in the beginning. If they offer three battery sizes I could see there being more margin in the middle size to allow upgrades to the largest battery via software locking.
To a certain extent, you're right, because Tesla is trying to please the street to have access to the capital markets at favorable terms, and so they won't let short term margins drop too much.
That said, ideally (from their perspective), it should be based on cost and
expected lifetime revenue. If they find that, say, 50% of S60 owners eventually go for the upgrade to 75 kWh, then they can figure that into what the sales price of the car is. For example, a $60k car with a $10k battery upgrade. If half of the customers eventually unlock it, then it's effectively a $65k car, and so they can determine whether to include a larger battery or not based on this expected revenue figure and what their cost is. If the battery were to cost less than $5k in every car, then on average, they come out ahead as a firm even if half of the owners never unlock it.
The Model 3 is no different, but given that it's going to be produced at a higher scale, and is a generally aggressive price point (though autopilot and other upgrades can make up for any lack of margin because a high percentage of owners will get those), maybe they hold off on a larger battery pack in order to not kill their financial performance in the short term.
If the base Model 3 gets a range increase, closer to say 250 miles,
and it has a larger battery pack that can be unlocked for nearly 300 miles of range, then I'm a buyer who will stick to the 250. It provides me the benefit of faster charging and less degradation over time. I think it's an extremely valuable feature. I would actually pay $1k for a bigger battery I couldn't access lol.