Yes there is a slight disadvantage at the moment for teams in the same league. However, your idea simply shifts this disadvantage to the lower leagues, so the ABBL gets a lot of benefit and the lower leagues get none.
"II teams don't directly compete against ABBL"
Yes they do in a sense. They compete whenever an ABBL team drops down to div 2. All the extra income that the ABBL teams will get from a seeded cup means more money for them to promote back up with.
Look at the following:
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There are 16 "teams" above, and they are in the order of best to worst.
In a seeded cup draw it will be:
1 v 16
2 v 15
3 v 14
4 v 13
5 v 12
6 v 11
7 v 10
8 v 9
Teams 1, 2, 3, 4, 5, 6 and 7 will almost definitely win. And either 8 or 9 could win, but let's say 8 wins.
So you will be left with the following teams:
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The next round will be:
1 v 8
2 v 7
3 v 6
4 v 5
And again the teams 1, 2, 3 and 4 will likely win.
Then you will have 1 v 4 and 2 v 3.
As you can see, in a seeded cup draw, the top 4 teams are almost always going to end up all the way to the semi finals without even having to have a very tough match.
This is hundreds of thousands of dollars that you are giving to ABBL teams for basically no effort at all.