I don't know if I am just not quite getting MVC, but I simply set a view-model object that contains the detail of the popup, and then when generating the view if that is currently set I populate the div containing the popup. CSS controls the look and positioning. 
So basically I am relying of Mithril's top-down re-render approach to conditionally build the view based on current application state -- it works really well and is immanently sensible to me.
I actually used a list of popup confirmation objects, so multiple confirmations can queue up.
In the controller, make a confirmation queue:
function Controller() {
    ...
    this.confirmation                   =[];
    ...
    }
In the view, create a confirmation view div if there's a confirmation queued, or an empty placeholder otherwise (Mithrils differencing works best if container elements don't appear and disappear from render to render):
function crtView(ctl) {
    ...
    return m("div", [
        ...
        crtConfirmationView(ctl),
        ...
        ]);
    }
function crtConfirmationView(ctl) {
    var cfm=ctl.confirmation[0];
    return m("div#popup-confirm",(cfm ? muiConfirm.crtView(ctl,cfm.title,cfm.body,cfm.buttons) : null));
    }
Then, whenever a confirmation is needed, just push a confirmation object into the queue and let Mithril's drawing system run and rebuild the view.
function deleteRecord(ctl,evt,row,idx,rcd) {
    var cfm={
        title   : m("span","Delete Customer: "+rcd.ContactName),
        body    : [
            m("p","Do you really want to delete customer "+rcd.CustomerId+" ("+rcd.ContactName+") and all associated appointments and addresses?"),
            m("p.warning", "This action cannot be undone. If this is a duplicate customer, it should be merged with the other record."),
            ],
        buttons : deleteButtons,
        proceed : "delete",
        index   : idx,
        record  : rcd,
        };
    ctl.confirmation.push(cfm);
    }
The confirmation object contains whatever properties that the confirm helper function crtView needs to create a confirmation view and then take action when the user clicks a button (or presses ENTER or ESCAPE, etc) -- just standard UI stuff that you abstract away into shared reusable components.
Note: Just in case anyone has questions about the array index, I have since moved away from using the array index to identify the record in the data model (when the delete is complete the array element should be removed). Instead I locate the affected record using database ID, which is resilient against intervening changes in the model, like sorting the list.