Oooooo, that is an interesting one. I would say it really depends on what sort of budget we're looking at, because if it's sufficiently high there is the ASUS laptop coming out where they will fully support upgrades of the GPU for two generations, or, alternatively, there are the external GPU options. It's also worth considering that they aren't quite as bad as they used to be in terms of relative price and so that stops being so much of an issue.
As far as taking the GPU back and forth, just keep hold of the original packaging and you should be fine. I took my old GPU out to replace it with a 980, and just left my old card stood on the shelf since it looks so nice, dropped (and caught it) a couple of times, took it back home, and then decided to bring it back to uni and install it, just wrapped in bubble wrap and it was fine; if you intend to just take the GPU back and forth just keep the old box.
But, if you're taking the GPU back and forth, unless it's relatively low budget and your current hardware won't be too much of a bottleneck (would expect it is) you're surely looking at having two sets of new hardware, at which point you may as well just go for a decent laptop.
Same goes for dekstop+cheap notebook, if you can handle the extra weight of the better laptop you may as well just go for the laptop.
If you were going down the desktop route what sort of thing would you be looking at, either specific hardware or general budget?
The thing about hauling it back and forth, is that surely, even if you go SFF, it will be expensive on a budget airline, even if you're only doing it once each way per year? I'm fine doing it with a full tower but that's because there is more than enough room in the boot and I'm driven to and from uni.