There are multiple reasons they do not offer the SuperCharger on the 40KW base model:
#1 - Marketing decision, and physical distance limitations on intial SuperCharger deployment sites:
Tesla is spacing the SuperChargers 150-200 miles apart, in order to blanket the country with as many as they can, while keeping the costs down, they are still a company in their infancy, they don't have the funds to deploy SuperChargers every 100 miles, which would be required for the 40KW model. Also, the 40KW version is designed as an "around town" EV, not for "road trips".. Right or wrong, that IS their thinking and logic, agree with it or not, it is what it is. Also, the smaller 40KW models will take longer to charge, if allowed to at SuperChargers, and the thinking is, they could be blocking their use for the road trippers, who actually need them,
#2 - Because of the #1, SuperChargers are not located in cities, they are on major interstates between cities, so they would be USELESS to most people who want to just extended their range within their local area.
also, because the SuperCharger is 90KW, this would be greater than 2C on the 40KW pack, which it could handle, however, it would affect the long term health of the pack if done many times, or multiple times per day.
This has a warranty implications for the 40KW model longterm, and they'd rather avoid the issue right now.
#3 - They have similar costs for all 3 models, and, they make the least profit on the base model.
At this moment in time, they are deeply, deeply in debt, this is not when they want to go out and sell a bunch of cars that they make little or no profit on. Right now, they need to make the more expensive models more attractive and increase the bottom line. If they ignore this basic fact, and sell you the 40KW base model you seem to insist on, they might not be around to design or sell the third generation more affordable model.
Its really a matter of survival now, and they are selling to the luxury market, that is not as price consous and not looking to save pennies on their luxury car purchase. Like it or not, this is the current situation, which can certainly change once they become more profitable by delivering cars and mass production.
The reality is, they don't really care if a Leaf owner buys a Model S, it's not their target market.
They are trying to capture %2 of the luxury car market, thats over 1,000,000 cars/year, if they can capture 20,000 cars/year of that market, for the next 2-3 years, they will be a success, and will be able to make it long term. and thats what's its all about for Tesla, right now. You don't have to accept this, but thats how it is, right now... If you can't afford the asking price, then don't buy one now, it's not like their are any better choices on the market now.