This is a tricky one.
For the GTC at least, we made it pretty clear in the rules that you are responsible for your own data, so in the end it's up to you as to how you handle it.
If it was me I'd do some research as to which was the most accurate method of recording my data, and then use that -- I wouldn't claim the higher number off either device, I'd figure out the 'best guess' as to my speed, and that's what I'd post.
However you won't be penalised for choosing the higher number from your two devices, and you won't even be penalised for using trackpoints (although we recommend that you select "trackpoints" as the calculation method if you do so).
In the end all these numbers are there to track your own progression, and I don't know about you but I'd rather race against a 100% accurate number in the past, rather than one that has been fiddled with in post-processing.
It's completely up to you though