Note that OP's #2 should be Z wasn't beaten by X, let alone Y.
Both versions are in principle ambiguous (maybe Y is less likely than X to beat Z, OR maybe Y is less likely than Z to be beaten by X. You can disambiguate by putting even before the one that Y is less likely to apply to...
Even X didn't beat Z, let alone Y
Z wasn't beaten by even X, let alone Y
...which both unambiguously assert that Y is far less likely to beat Z than X is (likely to beat Z). And given that (even) X didn't beat Z, the chance of Y beating Z is extremely low.
Note that OP's second example can also be disambiguated by repeating the preposition...
2a: Z wasn't beaten by X, let alone by Y
Y is even less likely than X to win
...WHICH IS NOT THE SAME AS...
Y is even less likely to be beaten by X than Z is (likely to be beaten by X)
It may help people see the ambiguity if they imagine saying OP's example sentences with very heavy stress on either X OR Z. Whichever one you put the heavy stress on (and/or precede by even is the one that let alone Y applies to.
X didn't beat Z, let alone Y
(if even X couldn't beat Z, Y would have no chance of beating Z)
Z wasn't beaten by X, let alone Y
(if X couldn't beat even Z, X would have no chance of beating Y)