@BrandonMcAlister
While it is possible to have two sets of routing services published using the publish routing services utility to the same enterprise portal (by using different values for -f option), only one set of routing services can be registered as utility services in your enterprise portal. The set that will be used as utility services is determined by the order in which you run publish routing services utility with the routing services published using the last run becoming the utility services in your enterprise portal.
So, in your case since you want services published from GDB1 to be treated as your "primary" routing services and services published from GDB2 as your "secondary" routing services, you need to run publish routing services utility using GDB2 first and then run publish routing services using utility using GDB1.
With regards to invalid dataset name error you are getting when you publish using GDB2, this is unexpected. Can you share the publishroutingservices.log file generated on your machine? Do not attach that log file in this post since that file can contain some sensitive information about your ArcGIS Enterprise deployment. You can send that file to me via email at dmandloi@esri.com
Thanks
Deelesh