Here is another suggestion:
I've seen customers use both the RFI and Contractor RFI modules. They do one of two things:
1. Create two projects, one for bidding and one for construction. This will keep the RFIs separate
2. Use one project, but number the bid RFIs differently, such as "B-###", to keep them separate from the RFIs generated during the construction phase.
Will keep searching for other options.