The question to ask is if Jungle Cruise didn’t exist would we have a Pirates? Maybe, maybe not.
But let's be honest. Jungle Cruise is mostly in this conversation because it was the most sophisticated ride at the park's opening. Now it's mostly around because people like it for its history (rather than its actual merits) and people would probably raise hell if they ever tried to remove it, not because they still really love it or identify it with Disneyland more than other attractions.
If you were to ask your average person to name their top 10 Disneyland attractions, I bet almost none of them would say Jungle Cruise.
It's an attraction that is iconically Disneyland, but it's not one that people have the same admiration for in the way they do for others like Pirates, IASW, etc.
I'm still not sure why thesis attractions can't be attractions that happened after a park's opening year. Thinking of several other examples:
Cedar Point: Park opened 1870, its thesis attraction is undoubtedly Millennium Force, which opened in 2000.
Magic Mountain: Park opened in 1971, thesis attraction is probably Superman: Escape from Krypton (1996).
Knott's: Farm started in the 20s, start of Ghost Town is harder to pin down but was there by the 50s, thesis attraction is probably Calico Mine Ride (60s)
Kings Island: Park opened in 1972, thesis attraction is the Beat, opened in 1979.
If a thesis attraction is one that encapsulates everything that a park does well and is unique to it, and parks and attractions evolve, it just seems arbitrary that a thesis attraction can only be from the park's opening year. Lots of parks don't fully understand what they are when they open, up to and including Disneyland. So if we look at this from the perspective of what attraction best fits what the park became, or what it is now, I think there are many better choices than Jungle Cruise.