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Thank you! Concerning Question 2: thanks for the easy counterexample. Looking at the more complicated $G/B$, we see that $B_i$ is a union of shifted cones indexed by words of length $i$ in the Weyl group. It's this kind of interesting behaviour that I would like to see generalized. I will edit Question 2 to mention this.
OOPS! Yes, you're right, thank you! But what if we assume that $X$ and $Y$ have trivial $\text{Pic}^0$, does it help? Is there a good description of the cokernel of $f^*: \text{Pic }X\to \text{Pic }Y$ (or just the next group in some long exact sequence extending $f^*$)?
Concerning the last reference: there is a complete description of toric vector bundles due to Klyachko 1989. In his long paper, among other things, he gives an iff condition for all rank 2 toric vector bundles to be split.
@Mohan: Sorry for being sketchy and giving the wrong answer. Unfortunately, I don't understand your argument. Is my "vector bundle" intuition wrong? Are you saying that $L_a \oplus L_{-a}$ does not depend on $a$?