After reading the FPN paper [1] again, I have realized that I have something mixed up. Let me share my conclusion, it seems that the MultiScaleRoIAlign is doing is mapping RoIs to which feature level then, in my case, Faster R-CNN will use this feature pyramid as an image pyramid to compute head.
I had FPN mixed up between Faster R-CNN and RPN implementation, refer to the paper to understand.
[1] https://arxiv.org/pdf/1612.03144.pdf