jai-ext is generally pretty slow at doing image processing with ROIs, part of it is due to the extra accesses and computation, however, it's not all:
Unlike JAI, operations specific for binary images are missing (e.g., scale, warp)
Extracting values from the ROIs with iterators is not particularly efficient, dedicated iterators for binary images should be developed
Thinking out loud, there is no support for marking/recognizing that a ROI tile is completely full or completely empty, which would help speed wise (the only ROI tiles that are interesting are the border ones)
jai-ext is generally pretty slow at doing image processing with ROIs, part of it is due to the extra accesses and computation, however, it's not all: