Firstly, I'm merely saying that Starting Tugs at the 4 and Khyri at the 3 puts us in a hole immediately when playing against conventional lineups. Small ball lineups are great when your opponent is tired, or is sagging a zone, or packing the paint. As your starting lineup such a lineup needs to be Wragge-esque and hit a lot of shots, cause the opponent is likely to grab most of the rebounds, get a good number of 2nd chance points, etc.
I am not "worried" about the Jays matador defense - it is what it is. Just don't make things worse by deliberately playing a guy (Tugs) in positions they are not suited for. With a true 4 (Hegner or Krampelj) starting we have sufficient size to keep opponents honest, to rebound, to protect the rim.
No one said anything about Khyri not playing, merely not starting at the 3. He'll get minutes in the normal rotation, just not 31 of them. Playing both Thomas and Bowen out of position provides the opponents great mismatch opportunities to exploit and potentially gets our guys tagged with early fouls. Thomas can still do his thing defensively...as he is a very good defensive player, but no one is indispensable.