There isn't a problem with how the game is set (maybe in the income difference between the top and 2nd division) but how many users are playing in each country.
In Spain -> a lot of teams -> higher level of competition -> forces teams to spend -> lower income
In Cyprus -> less teams -> lower level of competition -> doesn't force teams to spend as much -> higher income
But how does this imbalance affect other Leagues which aren't in direct competition? I'm not sure.
Yes, a team from the Spanish third division may be at a disadvantage on the Transfer List compared to a Cyprus third division team, but it doesn't affect the position of the Spanish team, because it affects all of the teams in his direct competition in the same way.
If he can't outbid the Cyprus team because the team has less money and working under a theoretical construction that every team in his division is of the same strength, then no team in his division can win that bid -> doesn't affect the competition.
Yes, it may be easier promoting in a smaller country but how does that affect the competition in Spain?
The only teams which may have a case are the B3 teams but they create a very small minority of teams.