Not sure if this question has ever been answered completely, but here is what I came up with.
Basically, you have to traverse the DOM to get to the individual checkboxes.
If SF has implemented a better solution in the last 10 years, please respond and let me know!

            function selectAll(thisTable) {
                console.log("selectAll(): " + thisTable);
                var vTBODY;
                var vTR = [];
                var vTD = [];
                var vINPUT = [];
                var checkboxIDs = [];

                // SFDC translates selectCheckboxes as:
                // <table><tr><td><input type=checkbox><input type=checkbox><input type=checkbox>...
                // The id of the selectCheckboxes is the ID of the table, passed into this function as thisTable
                // My (this file) component ID path to the pageblock containing the selectCheckboxes:
                var expr = "{!$Component.theForm.pb2}"; 

                // Completes the ID path to the selectCheckboxes we want to Select All
                // This allows you to reuse this function for multiple selectCheckboxes requiring Select All
                expr += ":" + thisTable; // note SF uses colon to concatenate path components

                // spit it out to confirm path
                console.log("B: expr: " + expr); // see how SF uses colons to separate IDs in the path

                // get all childnodes for the <table> (aka selectCheckboxes) then search for 'tbody'
                var allCheckboxes = document.getElementById(expr).childNodes;

                // look for nodeName = tbody, there is only one so Break when found
                for (i=0; i<allCheckboxes.length; i++) {
                    if (allCheckboxes[i].nodeName.toLowerCase() == "tbody") {
                        vTBODY = i;
                        break;
                    }
                }

                // get the TR in the tbody
                // There should only be 1 but which childNode?
                for (var i=0; i<allCheckboxes[vTBODY].childNodes.length; i++) {
                    if (allCheckboxes[vTBODY].childNodes[i].nodeName.toLowerCase() == "tr") {
                        vTR.push(allCheckboxes[vTBODY].childNodes[i]);
                    }
                }

                // get the TD in the TR
                // There should only be 1 but which childNode?
                for (var i=0; i<vTR.length; i++) {
                    var nodeLength = vTR[i].childNodes.length;
                    for (var j=0; j<nodeLength; j++) {
                        if (vTR[i].childNodes[j].nodeName.toLowerCase() == "td") {
                            vTD.push(vTR[i].childNodes[j]);
                        }
                    }
                }

                // get the INPUTs (type=checkbox) in the TD
                // There should be 1 for each SelectOption in the list
                for (var i=0; i<vTD.length; i++) {
                    var nodeLength = vTD[i].childNodes.length;
                    for (var j=0; j<nodeLength; j++) {
                        if (vTD[i].childNodes[j].nodeName.toLocaleLowerCase() == "input") {
                            vINPUT.push(vTD[i].childNodes[j]);
                        }
                    }
                }

                // add the INPUTs' (type=checkbox) ID to the list
                for (var k=0; k<vINPUT.length; k++) {
                    checkboxIDs.push(vINPUT[k].id);
                }

                // execute click event on each checkbox ID in the list
                for (var i=0; i<checkboxIDs.length; i++) {
                    document.getElementById(checkboxIDs[i]).click();
                    console.log("checkboxIDs[i]).checked: " + document.getElementById(checkboxIDs[i]).checked);
                }

                // since javascript executes so fast on the client to CLICK the checkboxes, and there
                // is latency reading the variable back from Saleforce, rerender the output section
                // a couple times to make sure the page shows the current state of the varable in Salesforce
                // Don't be afraid to include another rerender at 5 secs if necessary!
                // Or.. wrap this whole thing in a Promise()
                setTimeout(function() { rerenderOutput(); console.log("1 sec interval"); }, 1000);
                setTimeout(function() { rerenderOutput(); console.log("3 sec interval"); }, 3000);
            }