In general, bin size has only limited effects on the results, essentially spatial resolution and spatial correlation. Our rationale was that if bin size is similar to fragment length, two neighboring windows are "almost" independent, which is one of key assumptions of mosaics. In practice, it suffices that they are not significantly violated regarding the results. The only expection might be histone modifications, in which strong spatial correlation is expecdted. In this case, you might want to use MOSAiCS-HMM instead of MOSAiCS and MOSAiCS-HMM is already implemented in msoaics package as well.