Canon 4000D has a 18.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features Digic 4+ processor. On the other hand, Canon M6 has a 24.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features Digic 7 processor. Canon M6's sensor provides 6MP more than Canon 4000D's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Below you can see the 4000D and M6 sensor size comparison.
Canon 4000D and Canon M6 have sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Canon 4000D has 33% larger pixel area compared to Canon M6, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.