Clark flies in this episode, but only in the virtual world, and at the end of the episode he admits that he still can't willingly take flight in the "real world".
Clark's leap with Lois from the Daily Planet rooftop is very similar to the Super leap he had with Lois while under the influence of red kryptonite in Season Six's "Crimson". The only difference is that this time he flew around Metropolis with Lois rather than leaping over the city skylines with her.
The lighting in scenes set within the virtual world is odd. Even at the very beginning of the episode-throughout the episode, lights that come from outside or even from artificial lights all appear extremely bright, and some scenes that are inside and should not have lights like that seem to be coming from nowhere. The lighting in scenes set in the real world is more standard to the usual Smallville lighting (scenes set in Smallville/Kent Farm are colorful, everywhere else is 'dark').
The episodes title, "Collateral", means a borrower's pledge of specific property to a lender, to secure repayment of a loan and refers to Chloe and the agreement she made with the Suicide Squad. In the military, collateral damage is damage that is unintended or incidental to the intended outcome. The term means "unintentional or incidental injury or damage to persons or objects that would not be lawful military targets in the circumstances ruling at the time". This could also refer to Hawkman as collateral damage in the battle against evil.
The scene where Clark flies himself and Lois off the Daily Planet rooftop in the virtual world is somewhat reminiscent of the Superman/Lois flight in Superman: The Movie.