When comparing manual shuffling to true randomization, hand shuffling loses hard. What you are experiencing is what your hand shuffles SHOULD result in if they could be done properly. which is impossible. You'd have to shuffle for an hour staight to even get close.

Also, the sheer amount of games on Arena is orders of magnitude above paper Magic. So of course you will experience odd draws way more often. Do you rememnber that one game a year ago in paper Magic where you were totally screwed? That one game is a weekly occurence on Arena, probably mutiple times. Not because of coding issues, but simply by number of games. What you play on Arena daily amounts to weeks of paper Magic.