Actually you sound a little bit confused about clearing and applying transforms. They are completly different.
Clearing transforms means to reset the object transforms. You can do that by Alt+G, Alt+R, Alt+S.
Applying a transform means to make the transforms from object mode apply to the edit mode data and than clear the object mode transform. Thats done with Ctrl+A. If location transform is applied that means the origin (also the pivot point) jumps back to (0, 0, 0) leaving the geometry in place.
If you want to be able to clear your tranforms and have special positions to where they are moved when cleared, you need to have an Armature with bones. Only that will give you the control. Its also much more convenient to work with, when animating. You don't need any Weight Painting for an Armature to work. You can parent your object to the bones directly by selecting your object, then your armature, then go into pose mode and select your bone and press Ctrl+P and select Bone.
I think that is exactly what you want. It is perfect for robots with individual hard objects. I made this robot hand using this method and it is very easy to pose , animate and reset:
If you still want to go without an armature, even though it is handy... Apply All Transforms to Deltas works fine for me. It does exactly what you want too... I don't see how it messes up the rotations.
I suspect you have set your rotations to Quaternions. In that case Rotation to Deltas seems to fail miserably. Set it to Euler and deal with the gimbal lock and you will be fine I think.
I think you might have found a Bug, otherwise I just found it and will report it right now (EDIT3: done). Rotation to Deltas adds the current quaternion values to the existing values instead of multiplying the normal quaternion way. To get around it you can go into your object transform tab in the properties region and set the delta quaternion to (0, 0, 0, 0) instead of (1, 0, 0, 0) and then apply the Rotation to Deltas, that should work perfectly.