I'm using SourceTree v1.6.3.0 and BeyondCompare 4.0 Beta build 18746. Selecting "Beyond Compare" as the option for Diff | External Diff Tool in SourceTree works correctly with BC 4 Beta.
I currently use BC3 ... not tested with BC4beta
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It's possible ... (SRCTREE-WIN)
Within SourceTree - open Menu Tools->Options ... under Tab "Diff" select "Beyond Compare" as "External Diff Tool"
To use it, select the external diff -Button ...
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At least it was possible as I configured it (prae 1.3. Version) - haven't verified configuration on latest SRCTree
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Maybe the best is to add an issue at https://jira.atlassian.com/browse/SRCTREEWIN like I did with https://jira.atlassian.com/browse/SRCTREEWIN-1458
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