Warnings appear to be ignored when one uses InputAssistant, so is there a workaround to provide the user with some or all of the warnings?

Yes, there are several possibilities.

- StatusMessage command

It displays messages (including warnings) during InputScript processing. There are various options, please see documentation. There is now another option in Statusmessage: toText="xxx" inserts all messages into a text variable "xxxx" that can be displayed later on

- ProcessingOption TreatWarningAsErrors="On"  

- ProcessingOption MaxWarnings=x