I am sure the reason for creating a flange to hold the tube in place, is cost. For somebody building multiple boats, using a tool to install the tube may well be the fastest most cost effective method of installing a drain tube.
In all reality, for a wooden boat with a transom of sufficient thickness, a tube is totally unnecessary. All that is required for an expandable rubber plug to seal properly, is a round hole of the correct inside diameter. In theory, one could create a hole, seal the raw surface of the ID of the hole and insert the rubber plug directly into the hole. Only thing the tube does for you is provide a perfectly round hole of the proper size and create a surface which will wear well during repeated use.
The manner in which the tube is secured could vary greatly depending on the materials used for the tube and for the transom. Using one of the 3M products would be perfectly acceptable in a case with brass tube into wood/epoxy construction. As Tod has pointed out, if glued in, there is no need for a flange.