The metal-insulator transition (MIT) of bulk rare-earth nickelates is accompanied by a simultaneous charge ordering (CO) transition. We have investigated low-frequency resistance fluctuations (noise) across the MIT and magnetic transition of [EuNiO$_3$/LaNiO$_3$] superlattices, where selective suppression of charge ordering has been achieved by mismatching the superlattice periodicity with the periodicity of charge ordering. We have observed that irrespective of the presence/absence of long-range CO, the noise magnitude is enhanced by several orders with strong non-1/$f$ ($f$ = frequency) component when the system undergoes MIT and magnetic transition. The higher order statistics of resistance fluctuations reveal the presence of strong non-Gaussian components in both cases, further indicating inhomogeneous electrical transport arising from the electronic phase separation. Specifically, we find almost three orders of magnitude smaller noise in the insulating phase of the sample without long-range CO compared to the sample with CO. These findings suggest that digital synthesis can be a potential route to implement electronic transitions of complex oxides for device application.