Great question! It may be that the joints are being pulled into a deeper compression than they are comfortable. One idea to try is keeping more tension in the legs to keep the knees from closing as far as they can. When bending in from the straddle, you can keep pressing out against the foot locks to keep the heels from closing all the way to the hips, making space between the pelvis and the feet. You can keep the same activation in the Angel Bomb. While the heels might close to the hips in the drop, the activation of the muscles supporting the knee joint can help keep the ligaments or tendons taking too much pressure. If you are feeling discomfort through a joint, it’s typically a sign to make adjustments/build strength and is not the type of discomfort to ‘work through’.
Ground workouts videos that would help strengthen the hips, which then in turn can take care of the knee joints: Happy Hips!, Legs and Bands, Knee Grip workout, and Hip Stability.
Keep us posted and please take good care of those knees!