Usually in case of Functional analysis of differential methylation regions, the log-fold change corresponds to log fold change in gene expression associated with DMRs. For the differential methylation regions we only consider the absolute value of methylation difference for the Functional analysis.
Due the methylation data ranges from 0(unmethylated) to 1(fully methylated). Thus, we always don't use log-fold change although it is always used in gene expression analysis. We suggest using the DMR identification software such QDMR (for pre-defined regions) or SMART (for de novo identification of DMRs from BS-Seq data).