I have just read the CRT page on this, and at first reading this all seems very reasonable, and provides a lot of flexibility. So I don't know if I really understand what the issues are, but perhaps the following is the main one?
Using Braunston as an example, in previous years some/much of the visitor moorings have been used a winter mooring, and they are permanently signed as such on the towpath signs with date this dates. In addition part of the towpath on the Oxford (which I don't think is signed as visitor mooring) was set aside for winter mooring.
With this year scheme this will no longer happen, as with a few exceptions there will not be dedicated sites, just a permit to stop in one place for the period purchased (this I guess is the main crux of this years scheme?). However you will not be allowed to stop under the permit with 1km of a marina, so in Braunston's case as there is a marina there, you have to go 1km on either the GU or Oxford out of Braunston. Is this the issue, meaning that if you want to say somewhere like Braunston you would have to take up a winter mooring in the marina, as there will be no online wither moorings available there.
Is this what the issue is?
So