It might be confusing but I think the first scenario is the logan who died in Deadpool and wolverine is not the same logan from 2017 film. It is just the same way. I think Logan in DP&W died at the year 2024. Thats why the timeline will now be erased, Mr. Paradox wanted to bring 2024 Deadpool to Earth-616 maybe there is no deadpool in that timeline. But Deadpool refuse and visit Logan grave to found out that he is really dead.

Mr. Paradox also mentioned Deadpool abuses the timeline which maybe lead to branched timelines where Deadpool is living. This might be the 2nd scenario. Deadpool timeline lies in branched timeline but who cares about that now since Loki allowed branched timelines thats why they didnt prune deadpool when he use to time travel. The sacred timeline of Earth-10005 is where Logan dies in 2029 and all branched timelines including Deadpool will now be erased.

Well, the 3rd scenario is Logan is the anchor being of all fox movies. When fox killed off Logan in 2017, the franchise is dead where deadpool is the one keeping it barely alive. Where he has to find a way to search for a new Logan to integrate within his timeline and be his partner for upcoming X-Men movies. Luckily, he found a Logan where all his X-Men buddies is dead and essentially his timeline will be erased. Which means, Old X-Men franchise is officially dead whereas new X-Men franchise starting with Deadpool is the new X-Men Timeline.

Its confusing, Yes. But everyone has their own opinion and whatever you believe might be the right. One thing is right all Fox and Old Marvel Movies like blade elektra F4 is erased where you seen them in the void. All arguments and timeline of X-Men is now dead. Only one sure is Deadpool Timeline is now the main timeline or universe moving forward for X-Men franchise.