Their decision makes sense for the majority while also adding additional optional extras for those who want it - variax guitars aren't made anymore, they're old tech that L6 really didn't need to support with the new hardware but they will with the breakout box - You can keep your old helix until it comes out, it's not going to stop working because a new one came out.
The price of the helix would have been higher for all if they'd put the functionality inside the device, so you would be paying it anyway so it's not really an additional 220usd your original helix would have been baseline price + cost of nexus components and design/support at launch, may not have been the full baseline+220usd but wouldn't have been 'free'.
They've already said variax support will hopefully come with firmware version 1.5 (and the nexus box will probably be released alongside, that would be my guess - they're not going to release the box when it won't do anything as the firmware isn't ready for it).
The nexus port has been touted as something that will be able to do much more than just variax etc support, we'll learn what in the years to come