[multi-stage] Query timeout overwrite

Currently, the query option time doesn't overwrite correctly.

We should have:

user-config override should always be considered as the total time (maybe minus planning time, i will explain later)

with this in mind, all the current timeout configuration during query should also be considered as total time
all stages have a fixed timeout at an absolutely ts value = sys.currentTimeNano() + desiredTimeoutNano

if any stage hits this timeout, they will all agree to terminate.

See details in: https://github.com/apache/pinot/pull/9571#issuecomment-1278094979