So how should I book the tickets in order to have protection from missed connections for the whole of the journey?
Through tickets are no longer available unfortunately - unless you have something like an Interrail pass (which, incidentally, is currently 50% off).
You now have to split and therefore do not have any strict legal protection against missing your connection onto the Eurostar. Rail Europe do say that they are selling separate tickets, but they do not make clear the lack of protection for the connection.
Eurostar are generally quite reasonable about allowing you to rebook onto a later service, subject to the availability of seats - but at busy times, all remaining trains of the day may be sold out (and, being an airline on rails, no standing is allowed). And it is quite unlikely that either Eurostar or the TOC responsible would pay for a hotel.
The situation is a little better when connecting to/from Eurostar on the continent - if you miss a connection from one of the 8 Railteam operators to another, you can take the next service under the
"HOTNAT" scheme. This includes when travelling on split tickets, and does not require you to rebook.
A similar scheme also exists under the Agreement on Journey Continuation which 14 operators participate in. This does require rebooking though, and as an agreement between operators (rather than an explicit passenger right) it is no something which you can legally rely on.
Overall the position is that it is very difficult to obtain 100% legal protection, as you would have had in the past under a single CIV ticket. But in practice it is likely, albeit not guaranteed, that you will be allowed to travel on the next available service.
It does if the ticket to London is issued to London CIV
It is still a separate contract and so unfortunately there is no strict legal entitlement to travel on the next available service.