Other than that, highly overlapping probes may both have cross-hybridization potential. However, I would generally prefer to focus on regions with multiple (preferably, at least 4 probes) within a CpG Island. So, if the probes don't overlap (but are both in the same promoter for a gene), I think that can give you some additional confidence. Also, unless the cross-hybridization is a huge problem, using methylation thresholds (like average beta > 0.7 in one group and average beta < 0.3 in the other group) may help. Those are the sort of things that I have implemented in the COHCAP package.
Check this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909830/