Question: Bismark methylation for non-uniquely mapping BS-seq reads
I'm not certain about your piRNA approach, maybe others will be able to help with that question.
As for multi-mapped reads, from Bismark's documentation you can find the --ambig-bam flag:

For reads that have multiple alignments a random alignment is written out to a special file ending in .ambiguous.bam. The alignments are in Bowtie2 format and do not any contain Bismark specific entries such as the methylation call etc. These ambiguous BAM files are intended to be used as coverage estimators for variant callers.

It doesn't look like Bismark will return all of the multiple alignments, just a randomly selected one for a given read or read pair (this probably results from the way Bowtie2 handles multiple alignments within Bismark).