Total score 8:5
Clear superiority of 100-400 II in three indicators:
1.Almost twice the shutter speed when shooting with a mechanical shutter with R6, which is important for birds in flight to avoid rolling shutter and jagged wings.
2. Ability to zoom, which is useful when you are hiding and a bigger bird lands next to you.
3. Possibility of macro photos without having to put on extension rings.
In the remaining points 100-400 II there is a lead, but not by much.
4.lens stabilization gives advantage when using R6
5. Faster focus
6. Sharper (at least in my specimens)
7. Better work with 1.4x II
8. Watertight seals.
The advantages of a prime lens are:
1. Lighter
2. Constant weight balance because it is not a zoom.
3. A metal hood that is inseparable from the lens (with a zoom lens, it is possible to break the thread of the hood)
4. Less chance of dust getting inside because it's not a pump (this is my guess, no direct observations)
5. I guess it is more resistant in harsh conditions and that's why I prefer it for risky shots like during a storm and also because of its lower price.
In conclusion I have both, I bought the 100-400 II because it was a bargain and since then it has gradually replaced the 400 prime. The latter I use extremely rarely only on risky missions and it is permanently attached to my old camera 1D IV for R6 I prefer the 100-400 II, but if it costs two times higher, you can easily stay with the prime lens.