When I tried that a few weeks ago the result was major video blocking that was unacceptable. Unless there's something else to set, that does not work for me.
I'm pretty sure that for Blu-ray it is 24 fps, thus using the default setting in HB (i.e., whatever the source is) you should get compatible files. All of mine that have been successfully transcoded by HB have sync'd and played on my Apple TV.
I suspect the problem are the DTS tracks or the way tsmuxer handles DTS extractions. The only Blu-rays that have been difficult are those with DTS or DTS-HD audio. For instance, just this morning I tried to open the m2ts of Rush Hour 3 (DTS-HD audio) and HB crashed while opening the file. Every Blu-ray with AC3 audio has transcoded without problems.