Is it okay to use deeptools bamCompare (SES normalization) for comparisons across different ATAC-Seq datasets?
I would be very hesitant to use SES normalization in a case like this. We recommend that people run plotFingerprint first and see if there is good separation between the samples and only then using SES. I would not expect there to be drastic separation between the samples for ATAC-seq data, so I don't think it will work well. Our standard ATAC-seq normalization is RPGC (aka, "1x normalization"). That should work well for your use-case as well.

As an aside, if you really want to make statistically-backed comparisons between groups I can recommend the CSAW package.