In that case, export raw single frames if you plan on generating a LUT to then go back into AE to apply to the larger video segment. If you don’t have a lower end PC, AE can handle the m2ts straight from the blu-ray if it is h264 (as most newer releases and SW are) rather than MPEG2.
So, then you would export your matching frames from both sources for every scene (or every time you need a new LUT), use them with Dre’s tool, and then use the resulting LUT back in AE. Though I’m no expert and someone may correct me.