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WFR don't retroactively trigger for existing records so if any meet the criteria, no emails will be sent. To achieve that unfortunately, you have to mass update one of the rule criteria fields to FAIL the WFR criteria and then update it again to PASS the criteria.
This is not related to the OP, however I felt it might be worth noting if you wanted to query the Opportunity and get the StageName's "Type", you can infer it from these values: ---> SELECT Name, IsWon, IsClosed FROM Opportunity LIMIT 1
Have you tried contacting salesforce support? I really doubt such a feature would be available as it depends on the maturity level of the team, rather than having to micro-manage who updates the trace flag! I agree it's troublesome, but can't have that much freedom on multi-tenant platforms
Is this still the situtation in 2017? I am using a controller to return a recordTypeId. <input type="hidden" name="liveagent.prechat:CaseRecordTypeId" value="{!InboundRecordTypeId}" /> However, I still need to retrieve the exact Opportunity (provided by client using addCustomDetail(Id) and then route the chat to the correct skill based on the opportunity's type/name/subject