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1886 registered

I assume they assign the byes randomly? Or do they do it by first registered gets the first bye (sometimes it seems that way)?

Also, I've been thinking that when tourneys like this don't fill your chips should carry over from round to round but people who get byes should only carry through the round 1 starting stack. That way, the bye has no value (since they'll be a 2-1 underdog in round 2.

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It is random (I hope). Although this time - as was said above - you could still register after seating but if you did your chance of getting a bye is 0%.

As for your proposal, I disagree. There was a similar discussion for the WSOP HU event where lots of people said players without a bye should get half their buy-in back.
Personally I like it the way it is. It is not unfair as everyone has the same chance to get lucky.