And yes, my Cup run this season (though I love it) is probably the perfect illustration of why an entirely-randomly drawn Cup is an episode of bullshittery.
So what should it be based on? Based on your CR, you should have only faced bots so far and you have. Your Cup run this season is basically the same as what it would be if a non-random system were implemented.
Although I think the Hattrick system (country rank 1 vs. lowest remaining team, etc) is just as bullshitty for different reasons, I do think that the odds of bots surviving to round 4 would be fairly low since they'd be facing off against human teams in the third round for sure (unless more than 500 human managers manage to lose to bots at least).
I haven't thought enough of what would be better to give a great suggestion for an alternative. Maybe for each round when a bot remains, splitting the remaining teams into two pools, with the bots and lowest remaining teams into one pool, and matchups are drawn with the lower pool being home. I think once the bots are cleared random draws are probably okay. I just dislike the thought that we had an interleague game in round 2 and yet in round 4, there are 8 matches between d6 bots, plus probably more than a few VI vs. V bots (I didn't bother checking those).