Both Fujifilm X-E3 and Fujifilm X-T100 have 24.0 MP resolution sensors but Fujifilm X-E3's sensor is APS-C (23.6 x 15.6 mm ) and Fujifilm X-T100's sensor is APS-C (23.5 x 15.7 mm ).
Since Fujifilm X-T100's has a larger sensor area with the same resolution, this means that it also has a larger pixel area hence better light collecting capacity for a given aperture compared to Fujifilm X-E3.
Another difference between these two cameras is that Fujifilm X-E3's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the X-E3 and X-T100 sensor size comparison.
Fujifilm X-E3 and Fujifilm X-T100 have almost the same sensor size so none of them has any significant advantage over other in providing control over depth of field when used with same focal length and aperture.