Object manipulation pipeline: how to motion plan with the hand, but grasp without it...?

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That is odd. The table ought to be added to the planning scene separately, which would result in the gripper avoiding the table properly. Does the table show up as a polygon when you display the planning scene topic in rviz? If not, it's not being added to the planning scene. (You can add it using processCollisionGeometryForTable in collision_map_interface.cpp in the tabletop_collision_map_processing package.)

If the table is in the planning scene, then the move to the pre-grasp pose should be avoiding colliding with it. Disabling collisions between the grasp and the table is only done when checking for collisions with the final grasp pose, not the pre-grasp pose. So the pre-grasp pose should not be in collision with the table. We use move_arm to get to the pre-grasp pose, with collisions enabled between the gripper and the table, so there shouldn't be any collisions there.