I know operational emails are always exempt, so my plan is just to go through and turn all of them into operational emails if they're not already.
I was just trying to think through whether the Send Alert flow step is restricted by Communication Limits. To add a little color commentary, we have a custom API to our CRM, so when we use the "Send Alert" step, I simply have specify the email I want them to go to; I cannot select "Lead Owner" or "Account Owner" like you SFDC people (yes, I'm jealous...).
Sometimes I use tokens to pull in the email's from the fields I created for Lead and Account Owners (as you may know, Marketo's initial L.O. and A.O. are Marketo-controlled and cannot be affected by an API or anything but Marketo's native integrations).
I agree with Josh that I think that the Send Alert flow step might be it's own little thing, unaffected by the Communication Limits. But, regardless, you're right Adam - I just need to buck up and take the time to turn them operational.
Thanks though!