I actually agree this Long vs Short chain reference is confusing and that the LE chain of trust diagram is not especially clear. The length of chain has nothing to do with validity itself, it's just how they happen to be arranged currently.
I think of them as:
[Leaf] > R3 > ISRG Root X1 > DST Root CA X3 (we have taken to calling this the long chain)
and
[Leaf] > R3 > ISRG Root X1 (we have taken to calling this the short chain)
As an aside, I see on Certificate chain no longer includes ISRG Root X1? - #9 by guillerodriguez you may still have an important dependency on the "long chain" due to old clients not trusting ISRG Root X1 as the root, I would consider using certs from a different CA as the chain with DST Root CA X3 is going away soon (as you probably know) and now would be the time to decide/try out alternatives. Just getting DST Root CA X3 to work again is only a short term fix.