Each version of Pressflow is API-compatible with the same major Drupal version. For example, Pressflow 6 is compatible with all Drupal 6 modules. Pressflow 6 also integrates the SimpleTest system from Drupal 7 and the CDN support patch.
There are rare cases where the transaction will not be sufficient (e.g. the router or masks is empty), but I think those are rare enough to be worth trying this.
The lock_wait() in menu_rebuild() is harmful. During a menu_rebuild, we observed processes on web servers stuck for 30 seconds due to the lock_wait.
Since Pressflow is using a transaction, it seems unnecessary to wait the process until it has completed.