Handle should be level and perpendicular to direction of string travel, not necessarily the string.
Synchronized limbs don't necessarily show their tips even at full draw... or any other time... due to a variety of possible reasons.
Synchronized limbs will allow the string fulcrum to travel perpendicular to the handle as it's drawn. If limbs are of uneven strength, not synchronized, one of two things will happen...
1. If allowed to pivit, the bow will tip in the cradle. The strong limb will ride higher. Weakening the stronger limb until the bow comes to full draw without tipping is creating harmony between the limbs.
Or....
2. If your cradle shape and handle shape is such that it's not prone to tip in the tree, or if you elect to otherwise afix the handle solidly in the cradle, then keep a close eye on the fulcrum point on the string.... you will quickly see it pulled toward the stronger limb as it's drawn. It's a simple matter then to weaken the strong limb to allow the fulcrum point to travel perpendicular to the handle.
I draw a vertical line to simulate perfect string fulcrum travel, and then tiller the bow so that the hook on the string follows that line.... totally disregarding brace height measurements or profile.
These techniques will enable you to tiller/time odd-shaped bows with the same degree of confidence and accuracy as any others.
One more thing,... it is very important that you replicate your holds on bow and string as closely as possible. If you hold the bow with a torque-free grip, and neither healed or high, but allow the weight of the draw to pull evenly into your palm, it simplifies things and a cradle that spans the width of the grip will work well and you can watch the fulcrum as described in scenerio #2.
I have another idea that may be of considerable benefit and I'm going to work it out in the next few days. I'll let ya know if it works. My tree is always evolving too