I'm a little confused. Does the ruling state that both teams financed by a single entity couldn't join the UEFA, or will the league allow one of them to join it only? Plus what could be the reason for this ruling in the first place? I don't think there's much effect that it could cause towards the game other than the fact that there would now be more stakes to claim in major football leagues especially since you have more than one team on your payroll.
The UEFA rules state the following:
5.02 - If two or more clubs fail to meet the criteria aimed at ensuring the integrity of the competition, only one of them may be admitted to a UEFA club competition, in accordance with the following criteria (applicable in descending order):
SourceSo only 1 team could participate
Take a look at the rules in the link above, what is most worrying in these cases are possible influences to manipulate results
Imagine a scenario where 2 teams are owned by the same owner. Team A and team B, now imagine that a result for team A can directly affect team B, whether it's with qualification, a place in the round of 16, or even a direct confrontation
What should you do in this situation and how can you guarantee that the team's owner won't influence the result to benefit both teams?