Yes, the algorithm allows for skipping absent or Byzantine validators. It doesn't skip the height, it just progresses to the next round. In the end it's about getting more than 2/3 of commit votes.

You can prevote or precommit more than once per height (on different rounds), but a commit for a height must be the last signature for that height.

The sudden mass bonding is a problem for light clients doing a certain type of desirable SPV. We're considering options to mitigate this issue. One such option is to throttle the bonding and unbonding at the protocol level, or to introduce a second class of coin for validating and controlling issuance of it.