I agree on this one with you. Why can't bot players be left aside and take what's left? Of course it would give advantage to those who are in leagues with a lot of bots but then at the same time, they would actually have a chance to catch up quicker with the teams in the higher division and the number of bot teams probably (just probably because not sure on this) doesn't variate that much in the same division (lets say from V.1 to V.2). Just to strengthen the argument, national teams (U21 and NT) are worse off with bots picking randomly and this especially applies to weaker countries with fewer managers, where few good players taken on by bot teams can make all the difference for them! Parden my not excellent English, had a bottle of wine tonight ;]
but it makes it unfair, betwen the league, if you take your example, with V.1^and V.2 compare V.1 with V.60, which will be a better comparision.
Because if in V.1 a manager left, you will get a new one pretty fast, in V.60 you most likely have some bots because, it just get filled when V.1-V.59 are full of humans.