While I agree that the rafter parameters leave something to be desired, I would be VERY surprised if an SEO that just clips the bottom tip of the rafters is going to cause any noticeable slowdown. Usually, you have to get into the thousands of SEOs. In fact, I just tried placing a lot of rafters and used a slab to cut the bottom of them. I can't see any difference in performance.
Richard
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Richard Morrison, Architect-Interior Designer
AC26 (since AC6.0), Win10