[....]
I don't think there's something wrong with allowing teams financed by a single source into the UEFA really, it doesn't tarnish the reputation of the league in the first place, it allows more people to enjoy the game and more players to show their prowess, and most of all, it's going to keep the game of football alive!
That's quite a naive thinking. How do you think football fans would look at the competition between two sworn rivals and a competition between two sister clubs? The intensity of the game would be different at the very least. Another thing is that there will always be rumors of a rigged game that would affect the league's reputation. They don't want any of that so it's better to avoid it from ever happening.
I believe that's one factor that officials are considering in this specific scenario. If they are sister clubs, the owner may have his preference as to which team should have the edge in the championships. We can't deny the fact that there will be bias in this situation.
If the league will allow such arrangement, for sure, the owner in question doesn't really have full ownership for the other club. He may have influence but he is not the major stakeholder of the club.
Those rules were made in the past and I believe soon they won't be valid anymore as changes come. In my own opinion, all clubs should be eligible to participate in the Champions League whether are bonded to another club through ownership. And my reason is all players deserve to participate in the competition it will be a plus of how progressive they have been. As a football player, I won't be happy if put in the effort to qualify for the champions league and don't get to play.