Lets consider this hypothetical representation of the 64-bit time issue:
In `ROOT=/`, we have a `libA.so` with 32-bit time_t, and a `libB.so` with 32-bit time_t that depends on `libA` (ie: `libB.so` -> `libA.so`).
We rebuild package `A` with a special root (`ROOT=/tmp/new`) which has 64-bit time_t. We now have a `/tmp/new` with `libA.so` built for 64-bit time_t. We now want to build `B` for `ROOT=/tmp/new` with 64-bit time_t and have it link against the new `/tmp/new/lib/libA.so`.
But setting `ROOT=/tmp/new` doesn't cause us to use the `/tmp/new` to as our source to link against things. So (as it currently stands) we'll end up trying to link `libB.so` (64-bit time_t) against `/lib/libA.so` (32-bit time_t), and things just won't work.
If gentoo changes/extends ROOT (or adds something else like ROOT but used to locate dependencies for linking), then it could be a piece of a solution. But it sounds like it's pretty far from that in intention/practice right now.