Understanding the "relativeness" in RNA seq experiments
We cannot be sure about this. For all we know, they could have been sequenced to the same depth and there is a biological difference that drives the 1000x (ridiculously large) fold change.
See above


The only thing you can say for sure is that gene B is expressed twice as much as gene A in samples 1 and 2. That's what "relative" means - relative expression of genes within a sample.