Can't say to the Atlantic coast, but we started in Never after taking the regional train from Paris last summer, and it was roll-on roll-off for the bikes. The train cars had the hooks that stood the bikes upright. We stopped in Nantes, due to the logistics of crossing the bridge and in general spending another day and a half to get to the ocean and back to continue on with the next part of our trip. Do know if you take the buses across with a bike, reservations are required. There is also an on-demand taxi service, although I cannot recall the name right now.
We used this book:
https://www.amazon.com/complete-Loir.../dp/2737350018. Not the cheapest/easiest to find, but it had really good information and had the route broken down into suggested manageable chunks. We generally did 2-3 sections a day.
It is a nice route. Nothing too difficult, very touristy, easy riding in general. Lots of vineyards if that is your thing. Do know if you aren't used to French culture, and are not packing lunches, in the little villages lunch will only be available from 11-1 or so, and along that route there can be a decent gap form one village to another with a restaurant. Camping is very prevalent along the route, as are B&Bs/guesthouses/hotels/hostels that we stayed in. Most are very accommodating to cyclists, if they've got a Loire a Velo sticker or recommendation they generally have secure parking for bikes.
As to your actual question, EV6 and Loire a Velo are generally one in the same. That said, the LaV is regionally run, while EV6 is EU run, so in some areas they diverge for a few kilometers, especially where the region has an interest in running you through a town or tourist spot. I didn't find either route to particularly be better or worse, and generally followed the LaV signage, which is excellent. There are many areas on which you can ride either side of the banks that isn't explicitly called out, getting some sort of map is advised despite the good signange.