The method of the competition draw has no relevance when it comes to the match situation.
The seeding manipulations UEFA do in the Champions League and Europa Cup are designed to prevent the bigger clubs meeting each other too early and have the effect of ensuring that these clubs all make it through to the Quarter-Finals and beyond and make the competition 'more exciting'.
Whether or not seeding happens, the match day rule is that if the match is level on aggregate at Full time in the 2nd Leg, then if one team is leading on away goals, they have won. If not, then extra time is played. If at the end of extra time, the scored are level, then they look at away goals again. If one team hasn't won, then a penalty shootout takes place. This has been the procedure for many, many years and predates the seeding shenanegans...
Top Eleven is a game, that needs to be simple and transparent to the player. All the draws are done at the beginning of the season and laid out for all to see, and you can look at your progression right the way through to the Final. It doesn't need the complication of seeding, which needs human judgement to place teams in priority to enable the seeding to take place.