Both Fujifilm X-A2 and Fujifilm X-M1 have 16.0 MP resolution sensors but Fujifilm X-A2's sensor is APS-C (23.6 x 15.6 mm ) and Fujifilm X-M1's sensor is APS-C (23.6 x 15.6 mm ).
Since Fujifilm X-M1'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-A2.
One other difference between these two cameras that is worth mentioning is that Fujifilm X-M1's sensor doesn't have an 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 moiré occurring in certain scenes.
Below you can see the X-A2 and X-M1 sensor size comparison.
Fujifilm X-A2 and Fujifilm X-M1 have the same sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture.