In the end the UEFA club coefficients were a pretty good indication to how the end of the season played out. Here are the teams that will be in the 3rd round (non- champions path):
in the seeded pot in the unseeded pot
Benfica (17) Rubin Kazan (62)
Dinamo Kyiv (30) Zurich (103)
Panathinaikos (32) OB (104)
FC Twente (49) Trabzonspor (135)
Standard Liege (61) Timisoara (146)
Assuming all of the seeded teams win in this round, the 4th round will include:
SEEDED POT UNSEEDED POT
Bayern Munich (4) Dinamo Kyiv (30)
Arsenal (6) Panathinakos (32)
Olympique Lyonnais (13) FC Twente (49)
Benfica (17) Standard Liege (61)
Villarreal (19) Udinese (73)
Should Benfica lose their 3rd round match, Dinamo Kyiv will become a seeded team and hence would not be eligible to play Villarreal.
And should Villarreal win, they will go into the pot of second seeds for the group round. It's at least theoretically possible that Villarreal could play in a Europa League reunion group: Porto (1st seed), Villarreal (2nd), Bayer Leverkusen (3rd), and Dinamo Zagreb or Napoli (4th). And Villarreal could play FC Twente in the qualifying round!!