It should be possible to connect different tokens to each account funnel, i.e., if I have 3 funnels and I use three different CRM accounts because they are different businesses, I should be able to connect the CRM account of business 1 to the funnel of business 1, the CRM account of business 2 to the funnel of business 2 and so on, as well as do the corresponding mapping. Subject to each funnel having different channels connected, in the end they are separate.
