There's no reason why a win in the last race should count for more than a win in the first race. It's just a tacky way of increasing the likelihood that the title will go down to the wire.
I'm not opposed to differential points per se - it makes sense that Le Mans carries double WEC points, it makes sense that Bathurst carries double V8 Supercar Championship points. Same for the Indy 500. It could make sense for some events to carry double F1 championship points if you make them longer or more arduous than the others, or if you make them into double-headers like the Surfers Paradise event in V8SC.
You'd have to pick the right event(s), make sure it's something that's going to be well attended both by punters and by the great and the good in F1, and by high profile VIPs, so that it's clear to anyone watching that this is one of F1's flagship events and that's why it's worth more in championship terms than standard events. One thing I'd like to see with this kind of event is for F1 to make a bit of an effort in terms of presentation - if you watch the pre-race coverage of the Bathurst 1000, one of the things they as the tension builds is make each team bring their car out to the front of the garage and the main driver, co-driver and race engineer literally stand to attention in front of their vehicle for the cameras, and the cameras go down the length of pitlane introducing the teams and drivers to the TV audience (because they know that Bathurst gets a lot of extra viewers who don't watch the rest of the races). It's taken really seriously by everyone and a lot of effort goes into making sure the cars, the garages and the drivers and race engineers are looking absolutely pristine for the cameras. It's not a massive deal but it's indicative of the esteem in which that particular event is held - it's only double points but it's worth a lot more to the drivers than winning two normal V8SC races. In fact, some drivers would rather win Bathurst than win the title. F1 lacks a flagship event where everybody goes the extra mile to try to sell the sport, or at least present it in a good light, to a broader than usual audience. So I'd be in favour of doing that with, say Silverstone. Have a qualifying race on the Saturday afternoon over half a GP distance, with a few points on offer for the top three, then have a 1.5 times GP distance event on the Sunday, with 1.5 times the usual number of points awarded.