The effects of incomplete bisulfite conversion upon mapping efficiency
Bisulfite conversion efficiency has no effect on the mapping rate in bismark and similar tools. The reason is that the reads are fully bisulfite converted in silico before alignment to minimize mapping bias.

I would suggest that you play around with the settings handed to bowtie2, such as using local alignment and modifying the --score-min option to allow more mismatches. Alternatively, you might try a different aligner like bwameth, which will always do local alignment.