Yeah beta testing!!!
I found out the problem with the cloak images. It's a simple fix, the image canvas just needs to be reduced by a length of 40 and a height of 40. It has an excess "border" of 20 pixels on each size of the image. If I recall this was how it was done pre-AE, but as of AE the cloak image gets reduced by 20 on each side.
I'll let you know if I find anything else!
EDIT: Looking at this, one of the things I like is the fact that it looks like it is pretty simple to add our own stuff. It looks like people may make modules and/or add-ons for this because it's all controlled by the .xml.

This is so awesome rannl!
EDIT 2: You guys have probably thought about adding events to the Randomizer, like CE did before AE with the hazards. This would also allow the flagship to use combat augs and stuff. Maybe that will come later.
What I wanted to say though before I forget is that it is actually possible to change the events that happen AFTER defeating the Boss on phases 1 and 2, so different things will happen each time instead of the same "Just as you gain the upper hand..." text. You just change <event name="BOSS_ESCAPED"> to <eventList name="BOSS_ESCAPED"> and add different possibilities. So you could have some help come and repair the player's ship for example.
You can also cause what happens after you kill all of the flagships crew to do different things by making BOSS_AUTOMATED into an eventList. Of course with this new tool you could also make it a set thing that just gets randomized.