Fujifilm X-Pro3 has a
26.0MP APS-C (23.5 x 15.6 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor. On the other hand, Fujifilm X-E3 has a
24.0MP APS-C (23.6 x 15.6 mm ) sized CMOS X-TRANS III sensor and features EXR Processor III processor.
Another similarity between these two cameras is that both Fujifilm X-E3 and Fujifilm X-Pro3 sensors lack anti-alias (Low-Pass) filters. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moiré occurring in certain scenes.
Below you can see the X-Pro3 and X-E3 sensor size comparison.
Fujifilm X-Pro3 and Fujifilm X-E3 have almost the same sensor size, so neither of them has any significant advantage over the other in terms of providing control over depth of field when used with the same focal length and aperture.