Do you recommend any changes in the default settings while doing an analysis for histone modification versus transcription factor?

The type of protein and modification you look at can result in different types of peaks, like narrow versus broad peaks. Transcription factors tend to be narrow peaks, and that is the default setting for the peak calling pipeline.  Certain types of histone modifications can be more of a broad, or dispersed, peak.

If you're looking at histone modifications, you will want to set the broad peaks parameter under MACS2 to "True" before running a peak calling analysis.