The moveit_setup_assistant doesn't support doing that, but you can do it yourself by editing the files inside your moveit config package. Assuming the only thing that needs to change between your moveit packages is the SRDF, and you already have one SRDF for each robot-tool configuration. Then you can add "robot" and "tool" args to your planning_config.launch to look something like this:
<launch>
[...]
<arg name="robot" default="myrobot1"/>
<arg name="tool" default="mytool1"/>
<!-- Load universal robot description format (URDF) -->
<param if="$(arg load_robot_description)" name="$(arg robot_description)" command="$(find xacro)/xacro --inorder $(find myrobot_description)/urdf/$(robot)_$(tool).urdf.xacro" />
<!-- The semantic description that corresponds to the URDF -->
<param name="$(arg robot_description)_semantic" textfile="$(find myrobot_moveit_config)/config/$(robot)_$(tool).srdf" />
[...]
</launch>
... and then of course you need to edit the launch files that include planning_context.launch and pass through the robot and tool args. If you do a diff between your current "robot+tool" moveit configs and find things that are different between them other than the SRDF, you need to make them parametrizable as well, perhaps doing something like this in the launch files:
<include if="$(eval robot == 'myrobot1')" [...] />
