That’s the way it works. When a controller message is assigned to something it is no more passed through the corresponding MIDI in block. Imagine you would like to assign a CC64 controller to a synth parameter, but each time you activate this synth parameter with your controller you get sustained notes… probably what you would expect in this situation.
If you assigned a CC64 controller to Rig Manager (in order to assign it later on to a widget) or directly to a widget and want to generate a CC64, the idea is to map the corresponding widget to the CC64 parameter of a MIDI in block which will then produce it for you. If you need to activate two synth parameter with the same CC64 controller, assign it to one single widget mapped to a single plugin parameter and use a second widget mapped to another plugin parameter. Then put the two widgets in a widget group (see widget properties) and put one on top of the other in the panels view, if you want to see only one.
Regarding your Scriptlet, rather then using the MIDI input of the Scriptlet, you can simply add a control parameter and assign a CC64 controlled widget to it. A Scriptlet has to be considered as a plugin… well it is a plugin.