You should not use octopus merging in this situation. The Octopus join should only be used in cases where there are no merge conflicts or the conflicts are so simple that you can resolve them manually without the merge tools.
In your situation, you just have to do 2 regular merges, which will have the same effect as the octopus merge, but allow you to use your merge tools.
You can simply check the different versions of the branching heads manually and run the 3D merge tool twice to make it work with the osunos. But it would be the same process as the two ordinary mergers - just harder.
If you want to make an octopus merge to make your story look nicer, just do two merges and rewrite your story afterwards.