Had a few minutes to scan the updated numbers this morning. The issue is quality of contact. In two out, RISP situations the Twins have a 15.5 LD% and a 16.3 IFFB%. Those are both quite a bit worse than their overall numbers. That being the case, of course their BABIP in those situations is going to be horrible (.220).
Something that's worked out really well for this lineup is being aggressive early in the count. They haven't done that quite as much in these two out, RISP situations. Here's a look at their average pitches per plate appearance:
2 out, RISP PPA: 4.00 (656/164)
All other situations: 3.76 (4,949/1,316)
That may not seem like a huge difference, but keep in mind the team with the lowest overall pitches per plate appearance (the Twins) is at 3.79 and the highest (Texas) is at 4.10.