Reading code from https://github.com/apache/cassandra/blob/cassandra-2.1/src/java/org/apache/cassandra/db/compaction/LeveledManifest.java and comparing with behavior shown in https://gist.github.com/autocracy/c95aca6b00e42215daaf, the following happens:
Score for L1,L2,and L3 is all < 1 (paste shows 20/10 and 200/100, due to incremental repair).
Relevant code from here is
if (Sets.intersection(l1overlapping, compacting).size() > 0)
Since there will be overlap between what is compacting and L1 (in my case, pushing over 1,000 tables in to L1 from L0 SCTS), I get a pile up of 1,000 smaller tables in L0 while awaiting the transition from L0 to L1 and destroy my performance.
Requested outcome is to continue to perform SCTS on non-compacting L0 tables.